Integrating biogeographic and genetic approaches to investigate the history of bioluminescent colour alleles in the Jamaican click beetle, Pyrophorus plagiophthalamus

Bioluminescent colour in the Jamaican click beetle, Pyrophorus plagiophthalamus, is an ideal system for studies moving from gene to landscape to gain a holistic understanding of the molecular, ecological, and historical bases for adaptation. Previous studies have established the genetics of bioluminescent colour variation in the beetle to the level of the nucleotide base pair in the target gene luciferase. Three different luciferase colour alleles affecting ventral light organ colour [yellow-green (vYG), yellow (vYE), and orange (vOR)] were found segregating in P. plagiophthalamus populations. These alleles differ from each other in a number of replacement mutations (14 total), the majority of which (11) have a measurable effect on colour. Phylogenetic analysis revealed a long-term adaptive trend on Jamaica towards longer wavelength bioluminescence, culminating in the most recently derived vOR allele. Here, we further investigate the historical and geographic context of adaptive colour evolution by testing a vicariance model for the origins of the extant ventral light organ polymorphism: that the vOR allele arose and differentiated in an isolated deme on the east side of Jamaica before spreading westward. Comparisons of colour phenotypes, luciferase coding sequences, the third intron of the gene, mtDNA, and microsatellite data provided evidence for past population subdivision on Jamaica and ongoing gene flow, as has been found for other island endemics. However, the pattern of differentiation supported the allopatric divergence of vYG and vYE alleles. The vOR gene appears to have arisen relatively recently from a vYE precursor and postdates the period of major biogeographic isolation. We discuss the implications of the results for discerning ecological causation in the adaptive sequence from nucleotide to landscape to population change for bioluminescent colour.     

Spectral correspondence between visual spectral sensitivity and bioluminescence emission spectra in the click beetle Pyrophorus punctatissimus (Coleoptera: Elateridae)

The presence of two spectral mechanisms, near-ultraviolet and green (lambda(max)=545nm), is strongly suggested by electroretinographic visual spectral sensitivity curves obtained under dark and red chromatic adaptation conditions in the compound eyes of the click beetle Pyrophorus punctatissimus. The bioluminescence emission of the dorsal prothoracic lanterns is deep green (lambda(max)=543nm) and that of the ventral abdominal lantern is lime green (lambda(max)=556nm) in colour in P. punctatissimus. A broad green visual receptor would detect both deep green and lime green bioluminescent optical signals.     

Contribution to the knowledge of the click beetle genus Zorochros (Coleoptera: Elateridae) from Saudi Arabia

Examination of specimens of Elateridae revealed new generic and species records for Saudi Arabia. Zorochros amalec (Peyerimhoff) is recorded from Al Majardah, and Zorochros yosrae sp. n. is described as a new species from Thalouth Almanazar.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:E4B9EB99-BE55-4884-B220-BF9928926312     

Isolation and characterization of 16 microsatellite loci in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae: Scolytinae)

We isolated 16 polymorphic microsatellite loci in the mountain pine beetle (Dendroctonus ponderosae Hopkins) and developed conditions for amplifying these markers in four multiplex reactions. Three to 14 alleles were detected per locus across two sampled populations. Observed and expected heterozygosities ranged from 0.000 to 0.902 and from 0.100 to 0.830, respectively. Three loci deviated from Hardy-Weinberg equilibrium in one sampled population. One of these loci may be sex linked. These markers will be useful in the study of population structure in this important pest species.     

Isolation and characterization of microsatellite loci from two inbreeding bark beetle species (Coccotrypes)

We developed 14 microsatellite markers in Coccotrypes carpophagus and 14 in C. dactyliperda. These loci will be used for studying genetic structure and the level of inbreeding in populations in the Canary Islands and Madeira. As a result of long‐term inbreeding, genetic variability is relatively low in these bark beetle species. We found one to five alleles per locus in 29 C. carpophagus and 41 C. dactyliperda from various localities. Eleven of the markers developed for C. carpophagus amplified in C. dactyliperda and seven of the markers developed for C. dactyliperda amplified in C. carpophagus.     

Isolation and characterization of polymorphic microsatellites in the groundnut seed beetle,Caryedon serratus (Coleoptera,Bruchidae)

Caryedon serratus feeds on the seeds of four genera of wild Caesalpinioideae. It recently became a major pest of groundnut in Africa. To determine the extent of gene flow and isolation between wild and groundnut‐feeding populations, we isolated and characterized 10 microsatellite loci in this species. Polymorphism ranged from three to 15 alleles in the 80 individuals collected in four localities in Senegal on five host plants.     

Isolation and characterization of polymorphic microsatellite markers in Zabrotes subfasciatus Boheman (Coleoptera: Bruchidae)

Bruchid beetles of the genus Zabrotes (Coleoptera: Bruchidae) are important worldwide pests of legume seeds. Samples of Zabrotes subfasciatus and Z. sylvestris were collected from seeds of two Phaseolus species throughout Mexico to assess the role of host plant variation and plant domestication on the evolution of host use in this species. For this purpose six polymorphic microsatellite loci were isolated and characterized for the bruchid Z. subfasciatus. Cross‐species amplification tests were performed on Z. sylvestris and revealed that three loci amplified successfully and were polymorphic in this closely related species.     

Isolation and characterization of dinucleotide repeat microsatellites in Drosophila ananassae

Drosophila ananassae is a cosmopolitan species with a geographic range throughout most of the tropical and subtropical regions of the world. Previous studies of DNA sequence polymorphism in three genes has shown evidence of selection affecting broad expanses of the genome in regions with low rates of recombination in geographically local populations in and around India. The studies suggest that extensive physical and genetic maps based on molecular markers, and detailed studies of population structure may provide insight into the degree to which natural selection affects DNA sequence polymorphism across broad regions of chromosomes. We have isolated 85 dinucleotide repeat microsatellite sequences and developed assay conditions for genotyping using PCR. The dinucleotide repeats we isolated are shorter, on average, than those isolated in many other Drosophila species. Levels of genetic variation are high, comparable to Drosophila melanogaster. The levels of variation indicate the effective population size of an Indonesian population of D. ananassae is 58,692 (infinite allele model) and 217,284 (stepwise mutation model), similar to estimates of effective population size for D. melanogaster calculated using dinucleotide repeat microsatellites. The data also show that the Indonesian population is in a rapid expansion phase. Cross-species amplification of the microsatellites in 11 species from the Ananassae, Elegans, Eugracilis and Ficusphila subgroups indicates that the loci may be useful for studies of the sister species, D. pallidosa, but will have limited use for more distantly related species.     

Antennal sensilla of the click beetle,Melanotus villosus (Geoffroy) (Coleoptera: Elateridae)

The typology, number and placement of antennal sensilla of the click beetle Melanotus villosus (Geoffroy) (Coleoptera: Elateridae) were studied using scanning electron microscopy. On both the males and females the antennae are made up of the scape, pedicel and nine flagellomeres. Two types of basiconic sensilla, three types of trichoid sensilla, one type of styloconic sensilla, one type of chetoid sensilla, dome-shaped sensilla, grooved pegs, and Böhm sensilla all appear on the antennae of the beetles of both sexes, with the exception of trichoid sensilla type II, whose large number (average of 1635 hairs per antenna) was found only in male beetles. Sensilla trichodea type II evidently respond to the sex pheromone produced by the female beetle. Unlike the other two click beetles, studied up till now, Agriotes obscurus and Limonius aeruginosus, the trichoid and basiconic sensilla of M. villosus, whose proven or assumed function is olfactory, are located predominantly on the flagellomeres ventral extensions. It is assumed that the placement of the olfactory sensilla, mainly on the ventral side of M. villosuss antennae, and their more or less even distribution on the flagellomeres, can be seen as morphological adaptation of this species of insect, whose specific behavioural reaction of olfactory searching is flying, both before and after contact with an odour plume.     

Determination of Agriotes obscurus (Coleoptera: Elateridae) sex pheromone attraction range using target male behavioural responses

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The jump of the click beetle (Coleoptera, Elateridae)—a preliminary study

A preliminary account is given of the jump of the click beetle, Athous haemorrhoidalis (F.). The jump is normally made from an inverted position. It involves a jack-knifing movement whereby a prosternal peg is slid very rapidly down a smooth track into a mesosternal pit. The muscles which produce this movement are allowed to build up tension by a friction hold on the dorsal side of the peg. The anatomy of this jumping mechanism is briefly described. Ciné recording showed that the jump was usually nearly vertical and could exceed 0.3m in height; the beetle normally rotated several times head over tail during a jump. The jump was produced by a very rapid upwards movement of the beetle's centre of gravity during the jack-knifing action. In a typical jump, a 4 × 10⁻⁵ kg beetle could be subjected to an upwards acceleration of 3800 m/s⁻² (380 g). The minimum work done and the power output of the muscles causing jumping have been calculated. A simple mechanical model has been constructed to simulate a jump, and several possible ways in which the jumping mechanism could operate have been discussed.     

Isolation and characterization of microsatellite loci in the ground beetle Carabus nemoralis (Coleoptera,Carabidae)

We isolated and characterized 10 microsatellite loci in the ground beetle Carabus nemoralis (Coleoptera, Carabidae), an ubiquist species largely distributed in Europe. Polymorphism ranged from 3 to 12 alleles on the 30 individuals from the same locality examined.     

Isolation and characterization of microsatellite loci in the ground beetle Carabus problematicus (Coleoptera,Carabidae)

Six microsatellite loci were isolated from the ground beetle Carabus problematicus. The polymorphism ranged from two to 17 alleles and observed and expected heterozygosities ranged from 0.137 to 0.676 and 0.147 to 0.710, respectively.     

Isolation and characterization of microsatellites in a medicinal plant,Phyllanthus emblica (Euphorbiaceae)

• Premise of the study: Microsatellite markers were isolated and characterized in a medicinal plant, Phyllanthus emblica, to study population genetics for designing an effective in situ and ex situ conservation of genetic resources of the species. • Methods and Results: Six microsatellite markers were developed using an enrichment and magnetic separation protocol. They were characterized in two natural populations of P. emblica. Out of the six microsatellites, five showed polymorphism, with the number of alleles ranging from four to seven. Observed and expected heterozygosities ranged from 0.360 to 0.760 and 0.499 to 0.806, respectively. • Conclusions: The five polymorphic microsatellite markers will be useful for studying the genetic structure, reproductive biology, and for identification of clones and provenances of this important medicinal plant.     

Isolation and characterization of microsatellites loci in the lemon (Citrus limon)

This study reports the isolation and characterization of seven polymorphic microsatellite loci in Citrus. The loci were isolated from two libraries constructed from genomic DNA nonenriched for TC and AC repeats and enriched for AC repeats. These markers yielded four to nine alleles per locus (mean 6.14) in a survey of 32 Citrus cultivars. Average observed heterozygosity ranged from 0.43 to 0.72. The levels of polymorphism found in this study suggest that these microsatellite loci can become an important tool for genetic studies in Citrus.     

Peculiarities of the biotope distribution of click beetle larvae (Coleoptera, Elateridae) in the Irtysh River valley

The spatial distribution of Elateridae larvae in the Lower Irtysh valley has been analyzed. The larvae analyzed belonged to 19 Elateridae species inhabiting soils of the floodplain and the river terrace. It has been pointed out that the larvae of Paraphotistus nigricornis, Agriotes lineatus, Limonius parallelus, and Aplotarsus incanus are most tolerant to the regular spring flooding. It has been found that the species compositions of floodplains and terrace meadows are significantly different. As a rule, species with a wide tropical spectrum inhabit floodplain soils, including bush and forest habitats. At the same time, the terrace was dominated by species characteristic of open habitats, including the steppe zone. It has been revealed that the values of species diversity vary significantly in the floodplain and terrace plots, but the higher species richness (Menhinick index) was registered in the floodplain.     

Population genetic characterization of the endangered dung beetle Copris tripartitus (Coleoptera: Scarabaeidae) using novel microsatellite markers

The dung beetle Copris tripartitus (Coleoptera: Scarabaeidae) has long been considered an endangered insect in South Korea; the detection of recent population increases leaves its endangered status uncertain. Population genetic analysis subsequent to development of molecular markers is essential for establishing proper conservation strategies. In this study, we developed ten microsatellite markers specifically for C. tripartitus. Sixty-eight individuals of C. tripartitus collected from six South Korean localities were genotyped to validate these markers and preliminarily assess population genetic characteristics. Per-locus observed number of alleles, observed heterozygosity (H_O), and expected heterozygosity (H_E) ranged from 5–12, 0.499–0.958, and 0.54–0.743, respectively. All populations showed higher H_O than H_E, negative values of inbreeding coefficient, and, overall, no sign of recent population bottlenecks (excluding one population, Seosan). This suggests that C. tripartitus did not suffer from genetic drift and inbreeding, which are typically severe in small, isolated populations. Nevertheless, detection of only one of the two gene pools in some populations and resultant genetic subdivision into two population groups may suggest that the population size is not enough to cover both gene pools. Thus, a more extended period of protection may be required to ensure higher genetic diversity of widespread populations and achieve the long-term conservation goal.     

Population structure of an endemic vulnerable species, the Jamaican boa (Epicrates subflavus)

The Jamaican boa (Epicrates subflavus; also called Yellow boa) is an endemic species whose natural populations greatly and constantly declined since the late 19th century, mainly because of predation by introduced species, human persecution, and habitat destruction. In-situ conservation of the Jamaican boa is seriously hindered by the lack of information on demographic and ecological parameters as well as by a poor understanding of the population structure and species distribution in the wild. Here, using nine nuclear microsatellite loci and a fragment of the mitochondrial cytochrome b gene from 87 wild-born individuals, we present the first molecular genetic analyses focusing on the diversity and structure of the natural populations of the Jamaican boa. A model-based clustering analysis of multilocus microsatellite genotypes identifies three groups that are also significantly differentiated on the basis of F-statistics. Similarly, haplotypic network reconstruction methods applied on the cytochrome b haplotypes isolated here identify two well-differentiated haplogroups separated by four to six fixed mutations. Bayesian and metaGA analyses of the mitochondrial data set combined with sequences from other Boidae species indicate that rooting of the haplotypic network occurs most likely between the two defined haplogroups. Both analyses (based on nuclear and mitochondrial markers) underline an Eastern vs. (Western + Central) pattern of differentiation in agreement with geological data and patterns of differentiation uncovered in other vertebrate and invertebrate Jamaican species. Our results provide important insights for improving management of ex-situ captive populations and for guiding the development of proper in-situ species survival and habitat management plans for this spectacular, yet poorly known and vulnerable, snake.     

Isolation and characterization of 12 dinucleotide microsatellite loci in the anadromous fish Osmerus eperlanus (L.)

A subtractive hybridization method was used to isolate 12 dinucleotide microsatellite loci for the anadromous European smelt, Osmerus eperlanus (L.). Three to 17 (mean 8.08) alleles per locus were identified in the two populations screened, and observed heterozygosity ranged from 0.067 to 0.933. Loci in both populations showed significant deviations from Hardy-Weinberg expected frequencies. These 12 loci provide a good basis for investigation of O. eperlanus population structure.     

Phylogeny and biogeography of the Japanese rhinoceros beetle,Trypoxylus dichotomus (Coleoptera: Scarabaeidae) based on SNP markers

The Japanese rhinoceros beetle Trypoxylus dichotomus is one of the largest beetle species in the world and is commonly used in traditional Chinese medicine. Ten subspecies of T. dichotomus and a related Trypoxylus species (T. kanamorii) have been described throughout Asia, but their taxonomic delimitations remain problematic. To clarify issues such as taxonomy, and the degree of genetic differentiation of Trypoxylus populations, we investigated the genetic structure, genetic variability, and phylogeography of 53 specimens of Trypoxylus species from 44 locations in five Asian countries (China, Japan, Korea, Thailand, and Myanmar). Using specific‐locus amplified fragment sequencing (SLAF‐seq) techniques, we developed 330,799 SLAFs over 114.16M reads, in turn yielding 46,939 high‐resolution single nucleotide polymorphisms (SNPs) for genotyping. Phylogenetic analysis of SNPs indicated the presence of three distinct genetic groups, suggesting that the various subspecies could be treated as three groups of populations. PCA and ADMIXTURE analysis also identified three genetic clusters (North, South, West), which corresponded to their locations, suggesting that geographic factors were important in maintaining within population homogeneity and between population divergence. Analyses of SNP data confirmed the monophyly of certain subspecies on islands, while other subspecies (e.g., T. d. septentrionalis) were found to be polyphyletic and nested in more than one lineage. AMOVA demonstrated high level of differentiation among populations/groups. Also, pairwise F_ST values revealed high differentiation, particularly between South and West, as well as between North and South. Despite the differentiation, measurable gene flow was inferred between genetic clusters but at varying rates and directions. Our study demonstrated that SLAF‐seq derived markers outperformed 16S and COII sequences and provided improved resolution of the genetic differentiation of rhinoceros beetle populations from a large part of the species’ range.