Temporal and spatial mapping of red grouper Epinephelus morio sound production

The goals of this project were to determine the daily, seasonal and spatial patterns of red grouper Epinephelus morio sound production on the West Florida Shelf (WFS) using passive acoustics. An 11 month time series of acoustic data from fixed recorders deployed at a known E. morio aggregation site showed that E. morio produce sounds throughout the day and during all months of the year. Increased calling (number of files containing E. morio sound) was correlated to sunrise and sunset, and peaked in late summer (July and August) and early winter (November and December). Due to the ubiquitous production of sound, large‐scale spatial mapping across the WFS of E. morio sound production was feasible using recordings from shorter duration‐fixed location recorders and autonomous underwater vehicles (AUVs). Epinephelus morio were primarily recorded in waters 15–93 m deep, with increased sound production detected in hard bottom areas and within the Steamboat Lumps Marine Protected Area (Steamboat Lumps). AUV tracks through Steamboat Lumps, an offshore marine reserve where E. morio hole excavations have been previously mapped, showed that hydrophone‐integrated AUVs could accurately map the location of soniferous fish over spatial scales of <1 km. The results show that passive acoustics is an effective, non‐invasive tool to map the distribution of this species over large spatial scales.     

Isolation and characterization of polymorphic microsatellites from red coral grouper (Plectropomus maculatus)

The red coral grouper, Plectropomus maculatus, is a high value marine food fish species. We isolated the first set of 10 polymorphic microsatellites and examined their polymorphism in two related species: the Malabar grouper Epinephelus malabaricus and the brown‐marbled grouper Epinephelus fuscoguttatus. The average allele number of these 10 microsatellite DNA loci is 9.1/locus with a range of four to 17, whereas the expected heterozygosity ranged from 0.18 to 0.94, averaging 0.76. Five of the 10 markers amplified polymorphic and specific products in E. malabaricus, whereas only four were amplified in E. fuscoguttatus. These microsatellites could be applicable to captive breeding and to the studies on genetic diversity and population structure of grouper wild stocks.     

Isolation and Characterization of Nine Microsatellite Loci from the Hawaiian Grouper <Emphasis Type="Italic">Epinephelus Quernus</Emphasis> (Serranidae) for Population Genetic Analyses

The availability of variable genetic markers for groupers (Serranidae) has generally been limited to mitochondrial DNA. For studies of population genetic structure, more loci are usually required; particularly useful are those that are nuclear in origin such as microsatellites. Here, we isolated and characterized 9 microsatellite loci from the endemic Hawaiian grouper Epinephelus quernus using a biotin-labeled oligonucleotide-streptavidin–coated magnetic bead approach. Of the 20 repeat-containing fragments isolated, 15 had sufficient flanking region in which to design primers. Among these, 9 produced consistent polymerase chain reaction product, and 6 were highly variable. These 6 loci were all composed of dinucleotide repeats, with the number of alleles ranging from 6 to 18, and heterozygosities from 33.3% to 91.7%. The high levels of variability observed should make these markers useful for population genetic studies of E. quernus, and potentially other epinephelines.     

Twelve novel polymorphic microsatellite loci for the Yellow grouper (Epinephelus awoara) and cross-species amplifications

Yellow grouper (Epinephelus awoara) is a commercially important marine fish species. A dinucleotide-enriched genomic library of E. awoara was constructed using the method of FIASCO. Twelve loci were polymorphic in a test population with alleles per locus ranging from two to eight, and observed and expected heterozygosities per locus from 0.13 to 1.00 and from 0.20 to 0.86, respectively. Five loci significantly deviated from Hardy–Weinberg equilibrium and no significant linkage disequilibrium was found between pairs of loci. Cross-species amplification of these polymorphic microsatellite loci was performed in additional two related species. These polymorphic microsatellite loci would be useful for investigating genetic diversity of E. awoara and related species. L. Zhao and C. Shao have contributed equally to this work.     

Reproductive biology and management of two commercially important groupers in the SW Atlantic

The reproductive biology of Epinephelus morio (red grouper) and Mycteroperca bonaci (black grouper) were evaluated based on 533 specimens collected from artisanal fisheries landings in the Abrolhos Bank, Brazil, between May 2005 and September 2012. Sex ratio for the black grouper was 1:14 (n = 155 females and 11 males; 26.1–147 cm TL) and 1:10 for the red grouper (n = 334 females and 33 males; 15.0–96.0 cm TL). For both species, highest values of the gonadosomatic index (GSI) for females were recorded between July and October, indicating spawning during the austral winter. The length at first maturity (L₅₀) for females was estimated at 62.0 and 47.0 cm TL for the black and red grouper, respectively. Batch fecundity based on TL and TW ranged from 2 to 15.4^?10⁶ and 1.5 to 13.7^?10⁶ for the black and red grouper, respectively. Interviews with experienced fishers revealed that spawning seasons of both groupers are largely unrecognized. Results demonstrate a positive relationship between GSI peaks, lower temperatures and stronger winds. The information provided herein may help decision-making regarding fisheries management and conservation for E. morio and M. bonaci at various levels of governance in the Abrolhos Bank, the region with the largest and richest coralline reefs in the South Atlantic.     

Isolation and characterization of polymorphic microsatellite loci from a dinucleotide-enriched genomic library of seven-band grouper (Epinephelus septemfasciatus) and cross-species amplification

Seven-band grouper (Epinephelus septemfasciatus) is a commercially important fishery species. Sixty-six microsatellite loci were isolated from a dinucleotide-enriched genomic library of E. septemfasciatus. Twelve of these loci were polymorphic in a test population with alleles per locus ranging from two to five, and observed and expected heterozygosities per locus from 0.04 to 1.00 and from 0.28 to 0.76, respectively. Three loci significantly deviated from Hardy–Weinberg equilibrium and no significant linkage disequilibrium was found between pairs of loci after Bonferroni correction. Cross-species amplification of these polymorphic microsatellite loci was performed in additional two related species. These polymorphic microsatellite loci would be useful for investigating genetic resource of E. septemfasciatus and other related species. Lili Zhao and Changwei Shao have contributed equally.     

Gene variation and gene flow inOrchis morio (Orchidaceae) from Italy

Data are presented on genetic variation at 27 enzyme loci of the Green-Winged orchid,Orchis morio, in 18 population samples from Italy. The existence in Italy of two subspecies, i.e. subspp.morio andpicta, is not supported by allozyme data. No genetic heterogeneity was found betweenmorio-like andpicta-like samples and specimens. Moreover, morphological transition between the two forms was observed in different Italian populations. The parameters of genetic variability estimated forO. morio populations are consistent with those found among monocotyledon plants, and among those outcrossing, animal-pollinated and with wind-dispersed seeds. Genetic diversity of ItalianO. morio is mostly within populations. Correspondingly, low values of interpopulational genetic distance were found. This appears to be due to high levels of gene flow, which were estimated with different methods. The lack ofO. longicornu from Italian samples, as well as of any hybrid withO. morio (F₁, backcrossed or recombinant individuals) is demonstrated on the basis of genetic data. It is concluded that recurrent reports ofO. longicornu from Italy are due to confusion withO. morio or with otherOrchis species.     

Reproductive styles of shallow-water groupers (Pisces: Serranidae) in the eastern Gulf of Mexico and the consequences of fishing spawning aggregations

Synopsis Seasonal and spatial aspects of spawning for three commercially important grouper species in the northeastern Gulf of Mexico are detailed. These species — all of which are protogynous hermaphrodites - spawn in deep water (> 25 m for red grouper,> 40 m for gag and scamp), making it difficult to observe spawning behaviors without ROV or submersible support. They respond to intense fishing pressure in ways that are directly related to their respective reproductive styles. Species that aggregate appear to be more susceptible to such pressures than those that do not, as evidenced by marked skewing of sex ratios in favor of females. Gag, Mycteroperca microlepis, have suffered a drop in the proportion of males from 17% to 1% in the last 20 years; scamp, Mycteroperca phenax, have dropped from 36% to 18%; and red grouper, Epinephelus morio, which do not aggregate, have shown little change in the sex ratio over the past 25–30 years.     

Isolation and characterization of 20 microsatellite loci for an important tropical tree Shorea leprosula (Dipterocarpaceae) and their applicability to S. parvifolia

Shorea leprosula is an important timber tree in Southeast Asia. From a genomic library enriched for dinucleotide (CT) repeats, 20 polymorphic microsatellite markers were developed for this species. Polymorphism of these loci was evaluated in a sample of 24 adult individuals from a natural population. The number of alleles ranged from five to 15, and the observed heterozygosity ranged from 0.333 to 0.875. Probability of paternity exclusion, in the case where the mother is known, ranged from 0.285 to 0.784. These markers were also characterized for applicability in S. parvifolia; 16 loci were successfully cross‐amplified and showed high levels of polymorphism.     

An integrated genetic linkage map for eucalypts using RFLP,RAPD and isozyme markers

An integrated genetic linkage map for E. nitens was constructed in an outbred three-generation pedigree. Analysis of 210 RFLP, 125 RAPD and 4 isozyme loci resulted in 330 markers linked in 12 linkage groups covering 1462 cM (n=11 in eucalypts). The 12th linkage group is comprised of only 5 markers and will probably coalesce with another linkage group when further linked loci are located. Co-dominant RFLP loci segregating in both parents were used to integrate linkages identified in the male and female parents. Differences in recombination frequencies in the two parents were observed for a number of pairs of loci, and duplication of sequences was identified both within and between linkage groups. The markers were distributed randomly across the genome except for the RFLPs in linkage group 10 and for some loci showing segregation distortion, which were clustered into three regions of the map. The use of a large number of co-dominant RFLP loci in this map enables it to be used in other pedigrees of E. nitens and forms a basis for the detection and location of QTL in E. nitens and other eucalypt species.     

Assessment of genetic diversity and phylogenetic relationship among grouper species Epinephelus spp. from the Saudi waters of the Arabian Gulf

Understanding of fish genetic characterization plays a vital role in the conservation and utilization of fish genetic resources of grouper species. The present study was carried out to assess the genetic diversity and phylogenetic relationships in five grouper species, Epinephelus spp. from eastern Saudi Arabian coast using two molecular marker systems, inter simple sequence repeat (ISSR) and microsatellite (SSR) markers. In total, 219 individuals grouper specimens (Epinephelus tauvina, E. coioides, E. bleekeri, E. malabaricus, and E. areolatus) were genotyped with 10 ISSR and 11 SSR selected primers. The ISSR produced 94 DNA fragments, of which 44 were polymorphic with an average of 2.13 fragment per primer. While SSR primers generated 107 alleles, all of them were polymorphic with an average 9.72 per primer. ISSR and SSR techniques demonstrated a high level of gene diversity and genetic distances illustrated by UPGMA dendrograms among the grouper species. The results proved that the SSR markers were highly informative and efficient in detecting genetic variability and relationships of the Epinephelus spp.     

Intrageneric amplification of horse microsatellite markers with emphasis on the Przewalski's horse (E. pmewalskii)

Primer sequences flanking 13 microsatellite loci isolated from the domestic horse (E. caballus) were successfully used to amplify homologous loci in the Przewalski's horse (E. przewalskii). The results demonstrate that the level of polymorphism at all 13 loci in the Przewalski's horse was comparable to that in the domestic horse and the overall exclusion probability in the Przewalski's horse was calculated to be 0.9994. The results suggest that it should be possible to use E. caballus-derived microsatellite markers to provide parentage verification and additional valuable information to the captive management of E. przewalskii. The ability to amplify corresponding loci in the remaining five species of the genus was also confirmed, illustrating the general application of markers isolated from the domestic horse to the evaluation of polymorphism in the other six species of the genus.     

Isolation of 10 microsatellite markers for mongoose lemurs (Eulemur mongoz)

We present here 10 new microsatellite markers for the mongoose lemur (Eulemur mongoz), nine of which were isolated from E. mongoz and one from Lemur catta. At least 60 individuals were genotyped for each of the 10 loci. Mendelian inheritance at each locus was tested by genotyping five captive families with known pedigrees. All loci were polymorphic and demonstrated simple Mendelian inheritance. The microsatellite markers presented here will be useful for genetic surveys of wild E. mongoz, to gain insights into the genetic background of the captive population, and to aid in the conservation of the species’ genetic diversity.     

Development of novel tetra- and trinucleotide microsatellite markers for giant grouper <Emphasis Type="Italic">Epinephelus lanceolatus</Emphasis> using 454 pyrosequencing

Giant grouper (Epinephelus lanceolatus) is a commercially important species, but its wild population has recently been classified as vulnerable. This species has significant potential for use in aquaculture, though a greater understanding of population genetics is necessary for selective breeding programs to minimize kinship for genetically healthy individuals. High-throughput pyrosequencing of genomic DNA was used to identify and characterize novel tetra- and trinucleotide microsatellite markers in giant grouper from Sabah, Malaysia. In total, of 62,763 sequences containing simple sequence repeats (SSRs) were obtained, and 78 SSR loci were selected to possibly contain tetra- and trinucleotide repeats. Of these loci, 16 had tetra- and 8 had trinucleotide repeats, all of which exhibited polymorphisms within easily genotyped regions. A total of 143 alleles were identified with an average of 5.94 alleles per locus, with mean observed and expected heterozygosities of 0.648 and 0.620, respectively. Among of them, 15 microsatellite markers were identified without null alleles and with Hardy–Weinberg equilibrium. These alleles showed a combined non-exclusion probability of 0.01138. The probability of individual identification (P_ID) value combined with in descending order 12 microsatellite markers was 0.00008, which strongly suggests that the use of the microsatellite markers developed in this study in various combinations would result in a high resolution method for parentage analysis and individual identification. These markers could be used to establish a broodstock management program for giant grouper and to provide a foundation for genetic studies such as population structure, parentage analysis, and kinship selection.     

New microsatellite resources for groupers (Serranidae)

We characterized nine microsatellite loci and identified an additional 60 genomic regions containing microsatellites in the red hind grouper, Epinephelus guttatus. The nine loci were highly polymorphic, and primers designed from red hind genomic DNA produced a strong amplification product in a test panel of 16 other groupers in the genera Epinephelus and Mycteroperca collected from across the world. Most of the amplified regions were homologous to the red hind locus and a well‐defined microsatellite repeat was generally evident. The nine loci, together with the 60 uncharacterized microsatellite‐containing regions, provide a powerful tool for ecological and evolutionary studies in groupers.     

Number and size of clutch in Ptomascopus morio (Coleoptera: Silphidae: Nicrophorinae), with comparisons to Nicrophorus

Ptomascopus morio displays simpler parental care than Nicrophorus species. The effects of carcass size and clutch number on clutch size in P. morio were examined. Clutch size was related to carcass size. There was a negative correlation between number of clutch and clutch size for most sizes of carcass. Longevity of females was shorter when the carcass size was larger, such that total lifetime fecundity did not differ among carcasses of different sizes. The clutch size of P. morio was larger than that of Nicrophorus quadripunctatus. The clutch size of P. morio declined rapidly with repeated clutch production, but that of N. quadripunctatus was rather constant. This indicates that N. quadripunctatus maintains a more constant clutch size than P. morio over several reproductive attempts, although the former displays more complex parental care.     

Characterization of microsatellite markers for snouted treefrogs in the Scinax perpusillus species group (Anura, Hylidae)

We characterized eight microsatellite loci for snouted treefrogs in the Scinax perpusillus species group, a group of hylid frogs endemic to the Atlantic Coastal Forest of Brazil, and tested their utility in mainland and island species of the complex. All eight loci were polymorphic in one population of S. perpusillus; four of the loci showed excess homozygosity and three of those deviated from Hardy–Weinberg expectations, possibly due to null alleles, inbreeding, or population structure in sampled individuals. Six loci amplified and were polymorphic in S. arduous, S. argyreornatus, and S. faivovichi, but only one in S. alcatraz. These markers will be useful for quantifying effects of habitat fragmentation on population genetic diversity and connectivity in coastal and island populations of this threatened species group.     

Isolation and characterization of microsatellites in Echinochloa (L.) Beauv. spp.

Five primer pairs were developed that amplify microsatellite loci in three agronomically important Echinochloa (L.) Beauv. species: E. colona (L.) Link, E. crus‐galli (L.) Beauv. and E. crus‐pavonis (Kunth) Schultes. The microsatellites were tested on 24 individuals representing three species collected in rice fields from different geographical regions and revealed 3–7 alleles per microsatellite. Gene diversity [1 ? Σp_ij²] for four polymorphic loci within E. crus‐galli ranged from 0.12 to 0.61. Alleles at a fifth locus were useful in discriminating the species. The microsatellites should provide useful markers for intraspecific diversity studies and aid classification of species within this complex genus.     

Bats in bird nests in Australia: a review

Bats (Microchiroptera) utilize few types of bird nests as roosts. Ten species of bats (Molossidae and Vespertilionidae) were recorded roosting in the enclosed bottle-shaped mud nests of the Fairy Martin Hirundo ariel; two species (Vespertilionidae) were located in the hanging nests of scrubwrens Sericornis spp. and the Brown Gerygone Gerygone mouki; two species (Vespertilionidae) in the enclosed plant material nests of the Grey-crowned Babbler Pomatostomus temporalis and Fernwren Oreoscopus gutturalis; and one species (Emballonuridae) was recorded in the open cup-shaped nest of the White-rumped Swiftlet Collocalia spodiopygius. No information was available on the importance of bird nests as breeding sites and only one species, the Chocolate Wattled Bat Chalinolobus morio, has been recorded hibernating in a nest. Bird nests in Australia provide roosting habitat for four threatened bats and may be important to the conservation of these species.     

Cross‐species amplification of microsatellite loci in aphids: assessment and application

Despite the relative ease of isolating microsatellites, their development still requires substantial inputs of time, money and expertise. For this reason there is considerable interest in using existing microsatellites on species from which markers were not cloned. We tested cross‐species amplification of 48 existing aphid loci in species of the following genera: Aphidinae: Aphidini: Aphis and Rhopalosiphum; Aphidinae: Macrosiphini: Acyrthosiphum, Brevicoryne, Diuraphis, Illinoia, Macrosiphoniella, Macrosiphum, Metopeurum, Metapolophium, Myzus, Phorodon, Sitobion and Uroleucon and Neuquenaphidinae: Neuquenaphis. Our results show cross‐species application of known microsatellite loci is a highly promising source of codominant markers for population genetic and evolutionary studies in aphids.