Phylogeography and molecular phylogeny of Macaronesian island Tarphius (Coleoptera: Zopheridae): why are there so few species in the Azores?

Aim We used a phylogenetic framework to examine island colonization and predictions pertaining to differentiation within Macaronesian Tarphius (Insecta, Coleoptera, Zopheridae), and explain the paucity of endemics in the Azores compared with other Macaronesian archipelagos. Specifically, we test whether low diversity in the Azores could be due to recent colonization (phylogenetic lineage youth), cryptic speciation (distinct phylogenetic entities within species) or the young geological age of the archipelago. Location Macaronesian archipelagos (Azores, Madeira and the Canary Islands), northern Portugal and Morocco. Methods Phylogenetic analyses of mitochondrial and nuclear genes of Tarphius beetles of the Azores, other Macaronesian islands and neighbouring continental areas were used to investigate the origin of island biodiversity and to compare patterns of colonization and differentiation. A comparative nucleotide substitution rate test was used to select the appropriate substitution rate to infer clade divergence times. Results Madeiran and Canarian Tarphius species were found to be more closely related to each other, while Azorean taxa grouped separately. Azorean taxa showed concordance between species and phylogenetic clades, except for species that occur on multiple islands, which segregated by island of origin. Divergence time estimates revealed that Azorean Tarphius are an old group and that the most recent intra‐island speciation event on Santa Maria, the oldest island, occurred between 3.7 and 6.1 Ma. Main conclusions Our phylogenetic approach provides new evidence to understand the impoverishment of Azorean endemics: (1) Tarphius have had a long evolutionary history within the Azores, which does not support the hypothesis of fewer radiation events due to recent colonization; (2) the current taxonomy of Azorean Tarphius does not reflect common ancestry and cryptic speciation is responsible for the underestimation of endemics; (3) intra‐island differentiation in the Azores was found only in the oldest island, supporting the idea that young geological age of the archipelago limits the number of endemics; and (4) the lack of evidence for recent intra‐island diversification in Santa Maria could also explain the paucity of Azorean endemics. Phylogenetic reconstructions of other species‐rich taxa that occur on multiple Macaronesian archipelagos will reveal whether our conclusions are taxon specific, or of a more general nature.     

How many genes are there in plants (… and why are they there)?

Annotation of the first few complete plant genomes has revealed that plants have many genes. For Arabidopsis, over 26,500 gene loci have been predicted, whereas for rice, the number adds up to 41,000. Recent analysis of the poplar genome suggests more than 45,000 genes, and partial sequence data from Medicago and Lotus also suggest that these plants contain more than 40,000 genes. Nevertheless, estimations suggest that ancestral angiosperms had no more than 12,000-14,000 genes. One explanation for the large increase in gene number during angiosperm evolution is gene duplication. It has been shown previously that the retention of duplicates following small- and large-scale duplication events in plants is substantial. Taking into account the function of genes that have been duplicated, we are now beginning to understand why many plant genes might have been retained, and how their retention might be linked to the typical lifestyle of plants.     

Why are there so few fish in the sea?

The most dramatic gradient in global biodiversity is between marine and terrestrial environments. Terrestrial environments contain approximately 75-85% of all estimated species, but occupy only 30 per cent of the Earth's surface (and only approx. 1-10% by volume), whereas marine environments occupy a larger area and volume, but have a smaller fraction of Earth's estimated diversity. Many hypotheses have been proposed to explain this disparity, but there have been few large-scale quantitative tests. Here, we analyse patterns of diversity in actinopterygian (ray-finned) fishes, the most species-rich clade of marine vertebrates, containing 96 per cent of fish species. Despite the much greater area and productivity of marine environments, actinopterygian richness is similar in freshwater and marine habitats (15 150 versus 14 740 species). Net diversification rates (speciation-extinction) are similar in predominantly freshwater and saltwater clades. Both habitats are dominated by two hyperdiverse but relatively recent clades (Ostariophysi and Percomorpha). Remarkably, trait reconstructions (for both living and fossil taxa) suggest that all extant marine actinopterygians were derived from a freshwater ancestor, indicating a role for ancient extinction in explaining low marine richness. Finally, by analysing an entirely aquatic group, we are able to better sort among potential hypotheses for explaining the paradoxically low diversity of marine environments.     

The interactions of molecular chaperones with client proteins: why are they so weak?

The major classes of molecular chaperones have highly variable sequences, sizes, and shapes, yet they all bind to unfolded proteins, limit their aggregation, and assist in their folding. Despite the central importance of this process to protein homeostasis, it has not been clear exactly how chaperones guide this process or whether the diverse families of chaperones use similar mechanisms. For the first time, recent advances in NMR spectroscopy have enabled detailed studies of how unfolded, “client” proteins interact with both ATP-dependent and ATP-independent classes of chaperones. Here, we review examples from four distinct chaperones, Spy, Trigger Factor, DnaK, and HscA-HscB, highlighting the similarities and differences between their mechanisms. One striking similarity is that the chaperones all bind weakly to their clients, such that the chaperone–client interactions are readily outcompeted by stronger, intra- and intermolecular contacts in the folded state. Thus, the relatively weak affinity of these interactions seems to provide directionality to the folding process. However, there are also key differences, especially in the details of how the chaperones release clients and how ATP cycling impacts that process. For example, Spy releases clients in a largely folded state, while clients seem to be unfolded upon release from Trigger Factor or DnaK. Together, these studies are beginning to uncover the similarities and differences in how chaperones use weak interactions to guide protein folding.     

Why are there so few evolutionary transitions between aquatic and terrestrial ecosystems?

Insects and flowering plants have rarely invaded the sea. Explanations for this have traditionally centered on the unique shortcomings of these groups in the marine environment. We show, however, that transitions among terrestrial, freshwater, and marine environments are infrequent in all major plant and animal clades except tetrapod vertebrates. In general, well-adapted incumbents are at a competitive advantage over would-be invaders from a physically different habitat. Data on the times and places of transition are consistent with our contention that evolutionary transitions among physically different environments are most likely when incumbents in the recipient environment exist in a regime of low-intensity competition and prcdation, as in terrestrial communities of the middle Paleozoic or the land biotas of oceanic islands. Freshwater environments, in which inferred intensities of predation are lower than in most marine and terrestrial environments, offer less biotic resistance to invaders than do communities in the sea or on land. Most invaders respond to novel physical circumstances by shutting down their metabolic machinery, and therefore add to their subordinate status as competitors with active incumbents. Only active tetrapods, particularly those with high and endothermically driven rates of metabolism, have successfully overcome this limitation.     

The genomes and transposable elements in plants: are they friends or foes?

Transposable elements (TEs) are mobile genetic elements that are present in prokaryotes and eukaryotes. The ubiquity and abundance of these self-replicating entities, bereft of cellular function, had earned them the label of ‘genomic parasites’. However, the status of TEs has been revised, with ample genomic and biological evidence now portraying them as “genomic gold”. They are perceived as a major participant in the evolution of species. This review addresses the classification of TEs as well as their role and significance in the evolution of genomes, genetic diversity, gene regulation, and exaptation of contemporary species of the plant and animal kingdoms.     

Why are there so few freshwater fish species in most estuaries?

The freshwater fish assemblage in most estuaries is not as species rich as the marine assemblage in the same systems. Coupled with this differential richness is an apparent inability by most freshwater fish species to penetrate estuarine zones that are mesohaline (salinity: 5·0–17·9), polyhaline (salinity: 18·0–29·9) or euhaline (salinity: 30·0–39·9). The reason why mesohaline waters are avoided by most freshwater fishes is difficult to explain from a physiological perspective as many of these species would be isosmotic within this salinity range. Perhaps, a key to the poor penetration of estuarine waters by freshwater taxa is an inability to develop chloride cells in gill filament epithelia, as well as a lack of other osmoregulatory adaptations present in euryhaline fishes. Only a few freshwater fish species, especially some of those belonging to the family Cichlidae, have become fully euryhaline and have successfully occupied a wide range of estuaries, sometimes even dominating in hyperhaline systems (salinity 40+). Indeed, this review found that there are few fish species that can be termed holohaline (i.e. capable of occupying waters with a salinity range of 0–100+) and, of these taxa, there is a disproportionally high number of freshwater species (e.g. Cyprinodon variegatus, Oreochromis mossambicus and Sarotherodon melanotheron). Factors such as increased competition for food and higher predation rates by piscivorous fishes and birds may also play an important role in the low species richness and abundance of freshwater taxa in estuaries. Added to this is the relatively low species richness of freshwater fishes in river catchments when compared with the normally higher diversity of marine fish species for potential estuarine colonization from the adjacent coastal waters. The almost complete absence of freshwater fish larvae from the estuarine ichthyoplankton further reinforces the poor representation of this guild within these systems. An explanation as to why more freshwater fish species have not become euryhaline and occupied a wide range of estuaries similar to their marine counterparts is probably due to a combination of the above described factors, with physiological restrictions pertaining to limited salinity tolerances probably playing the most important role.     

Why are there so few resistance-associated mutations in insecticide target genes?

The genes encoding the three major targets of conventional insecticides are: Rdl, which encodes a gamma-aminobutyric acid receptor subunit (RDL); para, which encodes a voltage-gated sodium channel (PARA); and Ace, which encodes insect acetylcholinesterase (AChE). Interestingly, despite the complexity of the encoded receptors or enzymes, very few amino acid residues are replaced in different resistant insects: one within RDL, two within PARA and three or more within AChE. Here we examine the possible reasons underlying this extreme conservation by looking at the aspects of receptor and/or enzyme function that may constrain replacements to such a limited number of residues.     

Why are there so many carbohydrate-active enzyme-related genes in plants?

Plants contain far more carbohydrate-active enzyme-encoding genes than any other organism sequenced to date. The extremely large number of glycosidase and glycosyltransferase-related genes in plant genomes can be explained by the complex structure of the plant cell wall, by ancient genome duplication and by recent local duplications, but also by the recent emergence of novel and unrelated protein functions based on widely available pre-existing scaffolds.     

Ten years of AFLP in ecology and evolution: why so few animals?

Researchers in the field of molecular ecology and evolution require versatile and low-cost genetic typing methods. The AFLP (amplified fragment length polymorphism) method was introduced 10 years ago and shows many features that fulfil these requirements. With good quality genomic DNA at hand, it is relatively easy to generate anonymous multilocus DNA profiles in most species and the start-up time before data can be generated is often less than a week. Built-in dynamic, yet simple modifications make it possible to find a protocol suitable to the genome size of the species and to screen thousands of loci in hundreds of individuals for a relatively low cost. Until now, the method has primarily been applied in studies of plants, bacteria and fungi, with a strong bias towards economically important cultivated species and their pests. In this review we identify a number of research areas in the study of wild species of animals where the AFLP method, presently very much underused, should be a very valuable tool. These aspects include classical problems such as studies of population genetic structure and phylogenetic reconstructions, and also new challenges such as finding markers for genes governing adaptations in wild populations and modifications of the protocol that makes it possible to measure expression variation of multiple genes (cDNA-AFLP) and the distribution of DNA methylation. We hope this review will help molecular ecologists to identify when AFLP is likely to be superior to other more established methods, such as microsatellites, SNP (single nucleotide polymorphism) analyses and multigene DNA sequencing.     

Sexual dimorphism in birds: why are there so many different forms of dimorphism?

Variation in the extent of sexual dimorphism among bird species is traditionally attributed to differences in social mating system. However, there are many different forms of dimorphism among birds, and not all of them show an obvious correlation with social mating system. For example, recent work has shown that many highly polygamous species are, in fact, monomorphic, whereas many putatively monogamous species are dimorphic. In this paper we break up sexual dimorphism into subcomponents and then use comparative analyses to examine the pattern of covariation between these subcomponents and various aspects of sexual, social, and parental behaviour. Our first finding is that size dimorphism and plumage-colour dimorphism do not show the same pattern of covariation. Differences in size dimorphism are associated with variation in social mating system and sex differences in parental care, whereas differences in plumage-colour dimorphism are associated with variation in the frequency of extra-bond paternity. These results suggest that size dimorphism is associated with the sort of intrasexual competition described by traditional classifications of social mating system, whereas plumage-colour dimorphism is associated with cryptic female choice. However, when we break up plumage-colour dimorphism according to whether it is due to melanins, carotenoids or structural colours, we find that each category of plumage-colour dimorphism shows a different pattern of covariation. The correlation between overall plumage-colour dimorphism and the rate of extra-bond paternity is due to structural colours, whereas melanin-based dimorphism is associated with sex differences in parental care. The former result is particularly interesting given that new work suggests structural colours are associated with active sexual displays and the reflection of ultraviolet light.     

Juvenile-adult distribution of the bivalve Mya arenaria on intertidal flats in the Wadden Sea: why are there so few year classes?

Patchy distribution is frequently observed in benthic marine invertebrates. In order to indentify factors causing spatial patterns in the bivalve Mya arenaria, abundances of juveniles and adults, as well as death assemblages, were recorded on a 20-km scale in the intertidal zone of the Sylt-Rømø Bight. Both adults and juveniles exhibited pronounced patchiness. Shell length of juveniles rarely exceeded 2 mm in 1995, which was most likely a consequence of epibenthic predators truncating the size spectrum. Only a few yearclasses dominated the adult population. While the northern part of the Bight was colonized mainly by a 1993-cohort, most M. arenaria in the southern part were from the mid-1980s. It is hypothesized that epibenthic predation is a major cause of the lack of dense M. arenaria beds from other years. However, examination of the length–frequency distribution of death assemblages revealed that other unidentified causes of mortality exist. High abundances of adults were found in the mid and lower intertidal zone but not in the high intertidal zone. There was no indication that dispersal of M. arenaria spat in a landward or seaward direction contributed significantly to the observed distribution pattern, since spat occurred abundantly at all tidal levels except in the high intertidal zone. There was no evidence of negative adult-juvenile interaction. M. arenaria was not attracted by seagrass or projecting shell beds – the latter indicating erosion of the sediment – as abundances of adults and juveniles were generally low in these habitats. The effects of sediment type and of the bioturbating lugworm Arenicola marina were inconsistent. While adults were more abundant on muddy sand than on sand, recruitment was independent of sediment type. At all high density sites of adults (>50 ind m^–2), lugworm densities were below 5 ind m^–2, which may indicate a negative interaction. However, lugworm densities >30 ind m^–2 did not prevent relatively high M. arenaria recruitment of >500 ind m^–2.     

Maximum force production: why are crabs so strong?

Durophagous crabs successfully hunt hard-shelled prey by subjecting them to extremely strong biting forces using their claws. Here I show that, for a given body mass, six species of Cancer crabs (Cancer antennarius, Cancer branneri, Cancer gracilis, Cancer magister, Cancer oregonensis and Cancer productus) were able to exert mean maximum biting forces greater than the forces exerted in any other activity by most other animals. These strong biting forces were in part a result of the high stresses (740-1350 kN m(-2)) generated by the claw closer muscle. Furthermore, the maximum muscle stress increased with increasing mean resting sarcomere length (10-18 microm) for the closer muscle of the claws of these six Cancer species. A more extensive analysis incorporating published data on muscle stresses in other animal groups revealed that stress scales isometrically with the resting sarcomere length among species, as predicted by the sliding filament model of muscle contraction. Therefore, muscle or filament traits other than a very long mean sarcomere length need not be invoked in explaining the high stresses generated by crustacean claws.     

Male sterility in flowering plants: are plant growth substances involved?

Male sterility in flowering plants is of tremendous importance not only in molecular and developmental studies of stamen and pollen grains and evolutionary studies on the origin of dioecy, but also in its commercial application in hybrid seed production. This paper reviews the literature on the possible involvement of plant growth substances (PGSs) in male sterility, and in normal stamen and pollen development. Different experimental approaches on a number of male sterile systems and normal plants have shown that nearly all PGSs, i.e., gibberellins, cytokinins, auxin, abscisic acid, and ethylene, directly or indirectly influence the expression of male sterility. Analyses of endogenous PGSs have revealed that in male sterile plants the level and/or metabolism of more than one PGS is affected. These studies support the suggestion that it is the relative ratio of various PGSs, rather than any one substance, that is critical for normal stamen and pollen development. It is also proposed that gene-regulated male sterility is likely mediated through an altered balance of endogenous PGSs in developing flowers and stamens.     

Why are there so few examples of entomopathogenic fungi that manipulate host sexual behaviors?

For entomopathogenic fungi (EPF), it may be particularly advantageous to manipulate host behavior in order to increase conspecific encounters that facilitate transmission of conidia. To achieve this, some EPF apparently alter the chemical communication and signaling of insect sexual behavior, but there are very few documented examples. Here, we identify and discuss the few known examples and propose two categories of EPF-induced alterations in insect sexual behavior. First, EPF may induce changes in how healthy conspecifics of the opposite sex perceive and respond to the infected individual via chemical or visual cues, which promote the display of sexual behaviors towards the infected individual. Second, EPF may directly change sexual behavior of the infected individual to promote conspecific encounters. We conclude that the scarcity of observed examples is likely caused by the difficulty of detecting subtle changes in insect sexual behavior, but also because manipulation of host sexual behavior is a trait primarily present in understudied host-specific EPF.     

How are arthopod communities structured and why are they so diverse? Answers from Mediterranean mountains using hierarchical additive partitioning

Mountains are complex ecosystems supporting a great variety of taxa. Here, we explored the diversity patterns of arthropods in two mountains, pinpointing the spatial scale that accounts most for overall diversity variation, using an additive partitioning framework. Butterflies and Orthoptera were sampled in Rodopi (2012) and Grammos (2013) mountains. Diversity was partitioned into five hierarchical levels (mountain, elevational zone, habitat, transect and plot). We compared the estimated diversity values for each level to the respective permuted values expected by chance, for all species, as well as for species identified as “rare” or “common”. At broader spatial levels, the variation in total diversity was attributed to the beta diversity component: mountains accounted for 20.94 and 26.25% of butterfly and Orthoptera diversity, and elevational zones accounted for 28.94 and 35.87% respectively. At finer spatial scales, beta diversity was higher than expected by chance in terms of the Shannon index. The type of habitat was found to play a significant role only for rare orthopterans. Finally, common species were recognized for shaping overall species diversity. We highlight the importance of the spatial levels of elevation zone and then mountain position in conservation planning, due to the greater beta diversity recorded at this scale as compared to habitat or more finite scales. Monitoring programs might need to adapt different strategies with respect to the focal organisms, and consider patterns of common rather than rare species that found to drive the patterns of the entire community.