The biology and conservation status of the large hammerhead shark complex: the great,scalloped, and smooth hammerheads

Hammerhead sharks are among the most intriguing yet imperiled groups of large sharks globally. Until recently, our understanding of their biology, movements, diet, and life histories was challenged by a lack of studies. In recent years there has been a surge of published studies on this group of sharks, incorporating new information on age and growth, behavior, and the threats they face. Here we summarize and compare what is known on the biology and conservation of the three largest species of hammerhead sharks: the great hammerhead (Sphyrna mokarran), the scalloped hammerhead (Sphyrna lewini), and the smooth hammerhead (Sphyrna zygaena). We chose these species since they are the most well-studied of the hammerheads, and also because they are commonly captured in target and non-target fisheries worldwide. Thus, we also discuss population trends and the vulnerabilities of each species, and make recommendations for future studies on these fascinating and complex elasmobranch fishes.     

<Emphasis Type="Italic">Metschnikowia</Emphasis> mating genomics

Genes involved in mating type determination and recognition were examined in Metschnikowia and related species, to gather insights on factors affecting mating compatibility patterns among haplontic, heterothallic yeast species of the genus. We confirmed the universality of the special mating locus organisation found in Clavispora lusitaniae across and exclusive to the family Metschnikowiaceae (i.e., Metschnikowia and Clavispora). Timing of the divergence between idiomorphs was confirmed to coincide with the origin of the larger (CUG-ser) clade comprising the Debaryomycetaceae and the Metschnikowiaceae, exclusive of Cephaloascus fragrans. The sequence of the a mating pheromone is highly conserved within the large-spored Metschnikowia species, including Metschnikowia orientalis and Metschnikowia hawaiiana, but not Metschnikowia drosophilae or Metschnikowia torresii, which have a pattern of their own, as do other clades in the genus. In contrast, variation in α pheromones shows a more continuous, although imperfect correlation with phylogenetic distance as well as with in vivo mating compatibility.     

Characterization of the reproductive mode and life cycle of the whitish truffle <Emphasis Type="Italic">T. borchii</Emphasis>

Truffles are the fruiting structures of ascomycetes in the genus Tuber. Because of their economic importance, truffles have been cultivated for many years using artificially inoculated host plants. Nevertheless, the life cycle and reproductive mode of Tuber spp. are still poorly understood. In filamentous ascomycetes, sexual reproduction is genetically controlled by the mating-type (MAT) locus. Among Tuber spp., the MAT locus has been recently characterized in the black truffles Tuber melanosporum and Tuber indicum. Here, by using sequence information derived from these species and from a Tuber borchii expressed sequence tag (EST) showing similarity to the mat1 gene of Alternaria brassicicola, we embarked on a chromosome-walking procedure to sequence the complete MAT region of T. borchii. This fungus produces highly commercialized whitish truffles and represents a model species for addressing basic questions concerning the life cycle of Tuber spp. We show that T. borchii is heterothallic, as its MAT locus is organized into two idiomorphs, each harbored by different mycelial strains. The alignment of the MAT locus from black truffles and T. borchii reveals that extensive sequence rearrangements and inversions occurred between these species. Moreover, by coupling mating-type analyses to karyological observation, we show that mycelia isolated from ascocarps and mycorrhizae are formed by homokaryotic hyphae.     

Diversity of <Emphasis Type="Italic">A</Emphasis> mating type in <Emphasis Type="Italic">Lentinula edodes</Emphasis> and mating type preference in the cultivated strains

Diversity of A mating type in Lentinula edodes has been assessed by analysis of A mating loci in 127 strains collected from East Asia. It was discovered that hypervariable sequence region with an approximate length of 1 kb in the A mating locus, spanning 5′ region of HD2-intergenic region-5′ region of HD1, could represent individual A mating type as evidenced by comprehensive mating analysis. The sequence analysis revealed 27 A mating type alleles from 96 cultivated strains and 48 alleles from 31 wild strains. Twelve of them commonly appeared, leaving 63 unique A mating type alleles. It was also revealed that only A few A mating type alleles such as A1, A4, A5, and A7 were prevalent in the cultivated strains, accounting for 62.5% of all A mating types. This implies preferred selection of certain A mating types in the process of strain development and suggests potential role of A mating genes in the expression of genes governing mushroom quality. Dominant expression of an A mating gene HD1 was observed from A1 mating locus, the most prevalent A allele, in A1-containing dikaryons. However, connections between HD1 expression and A1 preference in the cultivated strains remain to be verified. The A mating type was highly diverse in the wild strains. Thirty-six unique A alleles were discovered from relatively small and confined area of mountainous region in Korean peninsula. The number will further increase because no A allele has been recurrently observed in the wild strains and thus newly discovered strain will have good chances to contain new A allele. The high diversity in small area also suggests that the A mating locus has evolved rapidly and thus its diversity will further increase.     

Inheritance and gene mapping of the white flower trait in <Emphasis Type="Italic">Brassica juncea</Emphasis>

Despite being a unique marker trait, white flower inheritance in Brassica juncea remains poorly understood at the gene level. In this study, we investigated a B. juncea landrace with white petal in China. The white petal phenotype possessed defective chromoplasts with less plastoglobuli than the yellow petal phenotype. Genetic analysis confirmed that two independent recessive genes (Bjpc1 and Bjpc2) controlled the white flower trait. We then mapped the BjPC1 gene in a BC₄ population comprising 2295 individuals. We identified seven AFLP (amplified fragment length polymorphism) markers closely linked to the white flower gene. BLAST search revealed the sequence of AFLP fragments were highly homologous with the Scaffold000085 and Scaffold000031 sequences on the A02 chromosome in the Brassica rapa genome. Based on this sequence homology, we developed simple sequence repeat (SSR) primer pairs and identified 13 SSRs linked to the BjPC1 gene, including two that were co-segregated (SSR9 and SSR10). The two closest markers (SSR4 and SSR11) were respectively 0.9 and 0.4 cM on either side of BjPC1. BLAST analysis revealed that these marker sequences corresponded highly to A02 in B. juncea. They were mapped within a 33 kb genomic region on B. rapa A02 (corresponds to a 40 kb genomic region on B. juncea A02) that included three genes. Sequence BjuA008406, homologous to AtPES2 in Arabidopsis thaliana and Bra032956 in B. rapa, was the most likely candidate for BjPC1. These results should accelerate BjPC1 cloning and facilitate our understanding of the molecular mechanisms controlling B. juncea petal color.     

Tandem duplications of receptor-like kinase genes reshaped the homologous chromosome 1 regions in <Emphasis Type="Italic">Oryza sativa</Emphasis> ssp. <Emphasis Type="Italic">indica</Emphasis> and <Emphasis Type="Italic">japonica</Emphasis> and their possible ancestral genomes

Plant receptor-like kinase (Rlk) genes form a large family, each encoding a protein with a signal motif, a single transmembrane region, and a cytoplasmic kinase domain. Various gene duplications have contributed to the establishment and expansion of the family. Here, we characterized the formation and evolution of the Rlk gene family in cultivated rice and their possible progenitors. Using wheat Rlk gene sequences, we identified orthologs from the genomes of domesticated rice subspecies Oryza sativa ssp. japonica and ssp. indica and their putative progenitors O. glaberrima and O. rufipogon. The four chromosome 1 orthologous regions ranged from 103 to 281 kb comprising 181 syntenic blocks with 75 to 100% sequence identity. These regions contained 11–19 Triticum aestivum kinases (Taks) and 10–15 Lr10 receptor-like kinases (Lrks) organized in clusters and 3–12 transposable elements (TEs). Dot plot analyses showed that the 4 regions had 21–37 conserved catalytic domains, mainly in protein kinases (PKs) and tyrosine kinases (TyrKs) in coupling state. Over 50% of the sequences of glaberrima/rufipogon and japonica/indica pairs were colinear, while japonica/indica displayed a marked sequence expansion with duplicated genes and TEs. A total of 2312 single nucleotide polymorphisms (SNPs) and insertion-deletions (INDELs) were identified between japonica and indica. Duplication of the Rlk genes in O. glaberrima and O. rufipogon occurred after the grass species radiation and before the divergence of O. rufipogon from O. glaberrima; the orthologous Rlk genes from O. japonica and O. indica duplicated after O. sativa separated from O. rufipogon; paralogs, obtained through extensive duplication, happened after the separation of rice from maize. Tandem duplication was the major factor contributing to the gene copy number variation and genome size expansion.     

Prolonged copulations as an alternative to male nuptial gift investment in the bushcricket <Emphasis Type="Italic">Letana inflata</Emphasis> (Orthoptera: Tettigoniidae)

In most bushcricket species, the male transfers a nuptial gift to the female during mating, consisting of a gelatinous spermatophylax attached to the paired ampulla with the sperm. The spermatophylax acts as a sperm protection device; during its consumption, the sperm are transferred into the female’s spermatheca. Males of the bushcricket Letana inflata (Brunner von Wattenwyl, 1878) show strongly extended copulation duration. When the pair finally separates, only an ampulla is visible at the females’ genital opening, but no spermatophylax. To better understand copulation dynamics in the absence of a spermatophylax, we studied copula duration and sperm transfer pattern. Our results show that in Letana inflata the missing spermatophylax is replaced by extended copulation, securing the transfer of sperm into the spermatheca.     

Mating Behavior and Basic Biology of <Emphasis Type="Italic">Haywardina cuculi</Emphasis><Emphasis Type="Bold">(</Emphasis>Diptera: Tephritidae), a Poorly Known Species Exhibiting High Variability in Copulation Duration

The natural history and mating behavior of a species of tephritid fruit fly in the poorly studied genus Haywardina are described for the first time. Haywardina cuculi Hendel larvae were recovered over four field seasons from infested fruit of Vassobia breviflora (Sendtn.) Hunz, which constitutes a new host plant record for this species. Recovered pupae emerged as adults over 183 days on average, suggesting that most individuals became dormant. Adult flies engaged in sexual activity as soon as two days after emergence, were highly promiscuous, and displayed large variability in copulation duration. As for most tephritid species in the subtribe Carpomyini, H. cuculi exhibited a resource defense mating system. Fly activity peaked around noon. Copulation could last from 9 min to 17 h, with most copulations beginning in the afternoon and lasting until the following day. We discuss the potential significance of copulation duration variability in light of mate guarding and sperm competition hypothesis and outline future research to understand the evolution of life history and these behavioral strategies.     

<Emphasis Type="Italic">Sporidiobolus johnsonii</Emphasis> and <Emphasis Type="Italic">Sporidiobolus salmonicolor</Emphasis> revisited

The relationship between Sporidiobolus johnsonii and S. salmonicolor was investigated using rDNA sequence data. Two statistically well-supported clades were obtained. One clade included the type strain of S. johnsonii and the other included the type strain of S. salmonicolor. However, some mating strains of S. salmonicolor were found in the S. johnsonii group. These strains belonged to mating type A2 and were sexually compatible with mating type A1 strains from the S. salmonicolor group. DNA–DNA reassociation values were high within each clade and moderate between the two clades. In the re-investigation of teliospore germination, we observed that the basidia of S. salmonicolor were two-celled. In S. johnsonii, basidia were not formed and teliospore germination resulted in direct formation of yeast cells. We hypothesize that the S. johnsonii clade is becoming genetically isolated from the S. salmonicolor group and that a speciation process is presently going on. We suspect that the observed sexual compatibility between strains of the S. johnsonii and S. salmonicolor groups and the possible genetic flow between the two species has little biological relevance because distinct phenotypes have been fixed in the two taxa and intermediate (hybrid) sequences for LSU and ITS rDNAs have not been detected.     

Cloning and functional characterization of the <Emphasis Type="Italic">SmNCED3</Emphasis> in <Emphasis Type="Italic">Salvia miltiorrhiza</Emphasis>

As one of the most important phytohormones, the abscisic acid (ABA) is often used to breed stress-tolerant crop lines with both higher yields and active ingredient contents. In higher plants, the 9-cis-epoxycarotenoid dioxygenase (NCED) has been found to be a regulatory enzyme involved in ABA biosynthesis. In research, the novel gene SmNCED3 was isolated from S. miltiorrhiza. The open reading frame of SmNCED3 was 1725-bp, and it was encoding 574 amino acids with a calculated molecular mass of 63,822 kDa, which was verified by the expression of SmNCED3 in E. coli. The deduced SmNCED3 amino acid sequence had high sequence homology with NCED sequences from other plants and contained a putative chloroplast transit targeting signal peptide at its N terminus. Phylogenetic analysis demonstrated that SmNCED3 had a closer affinity to NCED3 in Arabidopsis thaliana (AtNCED3). The 1732-bp 5′ flanking sequence of SmNCED3 was also cloned. It contained several phytohormone response elements, biotic or abiotic stress-related elements, and plant development-related elements. Real-time PCR revealed that SmNCED3 was highly expressed in leaves, and was strongly induced by exogenous ABA. A subcellular localization experiment indicated that SmNCED3 was located in chloroplast stroma, chloroplast membranes, and thylakoid membranes. The overexpression of SmNCED3 promoted ABA accumulation. These results indicated that SmNCED3 might be a rate-limiting gene regulating ABA biosynthesis, and improving abiotic stresses tolerance and active ingredient contents in plants.     

Horizontal transfer of the C-termini of <Emphasis Type="Italic">tccC</Emphasis> genes in <Emphasis Type="Italic">Photorhabdus</Emphasis> and <Emphasis Type="Italic">Xenorhabdus</Emphasis>

The high molecular weight insecticidal toxin complexes (Tcs), including four toxin-complex loci (tca, tcb, tcc and tcd), were first identified in Photorhabdus luminescens W14. Each member of tca, tcb or tcc is required for oral toxicity of Tcs. However, the sequence sources of the C-termini of tccC3, tccC4, tccC6 and tccC7 are unknown. Here, we performed a whole genome survey to identify the orthologs of Tc genes, and found 165 such genes in 14 bacterial genomes, including 40 genes homologous to tccC1-7 in P. luminescens TT01. The sequence sources of the C-termini of tccC2-6 were determined by sequence analysis. Further phylogenetic investigations suggested that the C-termini of 6 tccC genes experienced horizontal gene transfer events.     

Characterization of a <Emphasis Type="Italic">Pinus sylvestris</Emphasis> thaumatin-like protein gene and determination of antimicrobial activity of the in vitro expressed protein

Thaumatin-like proteins (TLPs) are pathogenesis-related proteins, which are involved in plant defense responses to pathogen infection. Expression of the Pinus sylvestris L. TLP gene is up-regulated by methyl jasmonate treatment and inoculation with Heterobasidion annosum. A full-length Pinus taeda TLP gene sequence was used to design PCR primers for amplification of the full-length TLP gene from P. sylvestris. A putative 705-bp open reading frame of TLP gene was cloned into Escherichia coli cells, and then subcloned into the overexpression vector pET100 using BL21 Star expression bacteria. Optimization of the expression of recombinant TLP was achieved by decreasing both expression temperature and IPTG concentration. The purified 24.6-kDa TLP shows antimicrobial activity against 12 fungal species.     

Variance in Female Reproductive Success Differentially Impacts Effective Population Size in the Short-Nosed Fruit Bat, <Emphasis Type="Italic">Cynopterus sphinx</Emphasis>

Effective population size (N _e) quantifies the effects of micro-evolutionary processes and the rate of loss of genetic diversity in a population. Several demographic and mating parameters reduce N _e. Theoretical studies elucidate the impacts of various demographic and mating system parameters on N _e, while empirical studies illustrate realized N _e for species with differing life histories and mating systems. However, effect of intra-specific variation in mating system on effective size remains largely unexplored. In this paper we investigated the effect of promiscuous and polygynous mating on N _e in two wild populations of the short-nosed fruit bat, Cynopterus sphinx. N _e/N (ratio of effective population size to census size) was lower than unity in both populations, and much lower for the polygynous population compared to promiscuous population. Elasticity analyses reveal that N _e/N was sensitive to deviations in the sex ratio. Variance in female reproductive success had a higher impact on N _e compared to variance in male reproductive success in the promiscuous population. However, for the polygynous population, impact of variance in male reproductive success on N _e was higher than that of variance in female reproductive success. Our results suggest that depending on mating system, different populations of the same species could have alternate evolutionary trajectories. The rate of loss of genetic diversity would be lower for the promiscuous population compared to the polygynous population. Our study is the first to highlight which parameters would most significantly impact population specific N _e under different mating systems.     

Effect of gut bacteria on fitness of the Chinese citrus fly, <Emphasis Type="Italic">Bactrocera minax</Emphasis> (Diptera: Tephritidae)

A likely symbiotic association between tephritid fruit flies and gut bacteria has been recognized since the beginning of the last century. However, direct evidence for a link between gut bacteria and fruit fly fitness is still limited or absent for many species. Similar to other tephritids, the gut of Bactrocera minax (Enderlein) (Diptera: Tephritidae) is known to contain bacteria throughout the life stage, but what, if any, impact these bacteria have on B. minax fitness is entirely unknown. In order to elucidate the effects of bacteria on the fitness of B. minax, resident bacteria were isolated from the adult gut using culture-dependent techniques. Adult fly diets were subsequently supplemented with three bacterial isolates (Klebsiella pneumonia, Citrobacter braakii and Pantoea dispersa), or bacteria were removed from flies by antibiotics treatment: untreated adults provided a control. Adult fitness parameters (male and female longevity, female fecundity, male copulation number) were measured for the two treatments and one control group. Results were complex depending on the fitness parameter measured and the bacterial species. Compared to the controls, antibiotic treated B. minax had significantly decreased fecundity, but male and female longevity was increased. When flies were fed diets supplemented with any of the three bacterial isolates, female fecundity was significantly enhanced. However, only Citrobacter braakii significantly increased male mating frequency than control males. The results show that gut bacteria directly influence fitness of B. minax, but impacts are dependent on the bacterial species and the fitness parameters measured.     

Fine mapping of the novel male-sterile mutant gene <Emphasis Type="Italic">ms39</Emphasis> in maize originated from outer space flight

A novel male-sterile maize mutant male sterility 39 (ms39) was obtained from offspring of the commercial hybrid Chuandan No. 9 that had been carried into outer space. A previous study demonstrated that ms39 is controlled by a single recessive nuclear gene, located on the long arm of chromosome 3. Here, we used 1073 mutant individuals derived from the (ms39?×?Mo17) F₂ population and sequentially developed new primers to identify markers supporting the fine mapping of ms39. A 365-kb region on chromosome 3 flanked by markers L8 and M30 at a genetic distance of 0.18 and 0.47 cM, respectively, was identified. According to the reference sequence of ZmB73_Ref-Gen_v4, 12 candidate genes were identified within the 365-kb mapping region. Based on cloning and sequence BLAST analysis of the 12 candidate genes, a four-base-pair deletion was found within the exon of Zm00001d043909, which encoded callose synthase12. This four-base-pair deletion resulted in a frameshift mutation in ms39, leading to the earlier termination of the coding protein, and ultimately caused abnormal performance of the callose synthase. Additionally, cytological observation was conducted on a sister cross population (ms39/ms39?×?ms39/Ms39). These observations showed that the tapetum cells of the ms39 mutant appeared abnormal from the dyad stage, and aborted microspores were observed during pollen development. These results lay the foundation for the cloning of ms39 and exploration of the molecular mechanism underlying aborted pollen development in ms39 maize.     

Revision of <Emphasis Type="Italic">Podocotyloides</Emphasis> Yamaguti, 1934 (Digenea: Opecoelidae), resurrection of <Emphasis Type="Italic">Pedunculacetabulum</Emphasis> Yamaguti, 1934 and the naming of a cryptic opecoelid species

Despite morphological and ecological inconsistencies among species, all plagioporine opecoelids with a pedunculate ventral sucker are currently considered to belong in the genus Podocotyloides Yamaguti, 1934. We revise the genus based on combined morphological and phylogenetic analyses of novel material collected from haemulid fishes in Queensland waters that we interpret to represent species congeneric with the type-species, Pod. petalophallus Yamaguti, 1934, also known from a haemulid, off Japan. Our phylogenetic analysis demonstrates polyphyly of Podocotyloides; prompts us to resurrect Pedunculacetabulum Yamaguti, 1934; and suggests that Pod. brevis Andres & Overstreet, 2013, from a deep-sea congrid in the Caribbean, and Pod. parupenei (Manter, 1963) Pritchard, 1966 and Pod. stenometra Pritchard, 1966, from mullids and chaetodontids, respectively, on the Great Barrier Reef, may each represent a distinct genus awaiting recognition. Our revised concept of Podocotyloides requires a pedunculate ventral sucker, but also a uterine sphincter prior to the genital atrium, a petalloid cirrus appendage, restriction of the vitelline follicles to the hindbody, and for the excretory vesicle to reach to the level of the ventral sucker. Of about 20 nominal species, we recognise just three in Podocotyloides (sensu stricto): Pod. petalophallus, Pod. gracilis (Yamaguti, 1952) Pritchard, 1966 and Pod. magnatestes Aleshkina & Gaevskaya, 1985. We provide new records for Pod. gracilis, and propose two new species of Podocotyloides, Pod. australis n. sp. and Pod. brevivesiculatus n. sp., and one new Pedunculacetabulum species, Ped. inopinipugnus n. sp., all from haemulids. Podocotyloides australis is morphologically indistinguishable from Pod. gracilis, and exploits the same definitive host, but is genetically and biogeographically distinct. It is thus a cryptic species, the first such opecoelid to be formally named.     

An overlooked hybrid between the two diploid <Emphasis Type="Italic">Chenopodium</Emphasis> species in Central Europe determined by microsatellite and morphological analysis

The presence and extent of hybridization within the Chenopodium album aggregate (Amaranthaceae) is still unclear. Although many hybrid combinations have been described, their existence in the field has never been systematically studied and verified. The main aim of this study was to ascertain the extent of interspecific hybridization between the diploid species C. ficifolium and C. suecicum using highly variable nuclear microsatellite markers. Due to the absence of such kind of molecular markers for the whole C. album group, we divided the analysis into two steps: (1) Eleven microsatellite loci designed for the closely related species C. quinoa were cross-amplified in five Eurasian species of the C. album diploid–polyploid complex, i.e. C. album s.s. (6x), C. striatiforme (4x), C. strictum (4x), C. ficifolium (2x) and C. suecicum (2x); (2) For the detection of interspecific hybridization between C. ficifolium and C. suecicum, we sampled 480 individuals from five localities in Central Europe. We also investigated morphological differences between the parental taxa and their hybrid and devised a key for their determination. Analysis of variation in microsatellite loci using Bayesian methods, PCoA and Neighbour-joining tree identified 32 F1 hybrids. These F1 hybrids, described here as C. paradoxum Mandák, formed a cluster between well-differentiated parental species, combining the morphological characters of both their parents. Moreover, genetic analyses also recognized several F2 or backcross hybrids, whose delimitation, mainly from C. suecicum and F1 hybrids, based on morphological characters, is problematic.