Elucidation of the speciation history of three sister species of crown-of-thorns starfish (Acanthaster spp.) based on genomic analysis

The crown-of-thorns starfish (COTS) is a coral predator that is widely distributed in Indo-Pacific Oceans. A previous phylogenetic study using partial mitochondrial sequences suggested that COTS had diverged into four distinct species, but a nuclear genome-based analysis to confirm this was not conducted. To address this, COTS species nuclear genome sequences were analysed here, sequencing Northern Indian Ocean (NIO) and Red Sea (RS) species genomes for the first time, followed by a comparative analysis with the Pacific Ocean (PO) species. Phylogenetic analysis and ADMIXTURE analysis revealed clear divergences between the three COTS species. Furthermore, within the PO species, the phylogenetic position of the Hawaiian sample was further away from the other Pacific-derived samples than expected based on the mitochondrial data, suggesting that it may be a PO subspecies. The pairwise sequentially Markovian coalescent model showed that the trajectories of the population size diverged by region during the Mid-Pleistocene transition when the sea-level was dramatically decreased, strongly suggesting that the three COTS species experienced allopatric speciation. Analysis of the orthologues indicated that there were remarkable genes with species-specific positive selection in the genomes of the PO and RS species, which suggested that there may be local adaptations in the COTS species.     

Morphology of spines and spine joint in the crown-of-thorns starfish Acanthaster planci (Echinodermata,Asteroida)

Summary Morphology and movement of the spines of Acanthaster planci were studied. All surfaces of the animal are covered with spines. The spines on the aboral surface are cylindrical with sharp tips. The spines on the oral surface are flat; they bend over to cover the mouth and the ambulacral grooves when these soft parts are stimulated. Those on the side of the animal make a barrier of crossed spines. Thus the structure and movement of the spines are well-adapted for defense.The junction between the primary aboral spine and its pedicel makes a movable joint. The ultrastructure of the connective tissue at the joint was studied. The connective tissue is mainly composed of collagen fibers. Presumed neurosecretory cells with processes which are filled with electron-dense granules of 0.2 m diameter were found between collagen fibers. Muscle fibers are mainly found in the connective tissue at the central holes. These observations support the view that the joint connective tissue has catch properties.     

eDNA detection of corallivorous seastar (Acanthaster cf. solaris) outbreaks on the Great Barrier Reef using digital droplet PCR

Coral Reefs - Coral loss through consumption by corallivorous crown-of-thorns seastars (CoTS, Acanthaster spp.) is a major contributor to the coral reef crisis in the Indo-Pacific region. The...     

Evaluation of a crown-of-thorns starfish (Acanthaster planci) control program at Grub Reef (central Great Barrier Reef)

A crown-of-thorns starfish control program was conducted at Grub Reef (central Great Barrier Reef) in an area (0.64 km²) which encompassed 53 individual patch reefs. During a two week period, 15 divers injected 3175 starfish with copper sulphate. The program was considered unsuccessful. Although starfish abundance had declined significantly after the control efforts, biological surveys indicated that a relatively large number of starfish remained. The surveys also indicated a general decline in the number of starfish along the reef perimeter, outside the control area. The total cost of the control program was $35 per starfish. These results have important implications for the implementation of future control programs and highlight the need to undertake before and after biological surveys to assess the effectiveness of the control efforts.     

History and dynamics of the crown-of-thorns starfish Acanthaster planci (L.) in the Suva area,Fiji

Annual recruitment of Acanthaster planci over a 13 year period in a known juvenile refuge substratum on Suva Reef was very patchy in time and space. Macroscale recruitment events resulted in outbreaks over many thousands of hectares over 100 km of coastline whereas localised but intensive mesoscale events resulted in concenrated aggregations over areas of several tens of hectares. A very low level of recruitment occurred in most years but three intensive, macroscale recruitment events occurred in 1977, 1984 and 1987, and two localised but intensive recruitment events occurred in 1982 and 1983. Annual recruitment of A. planci between 1975–89 had no overt relationship with rainfall events, as proposed in the terrestrial run-off hypothesis on the cause of primary out-breaks. Growth rates within monitored cohorts were highly variable, but mean growth rates of two cohorts 1984 and 1987 were relatively similar. Mortality rates of three monitored cohorts were variable. Longevity of the 1977 cohort was 7–8 years, while that of the 1984 cohort was 2–3 years. Mortality of the 1987 cohort has been low to date (i.e. 4 years of age). Disease, attributed to an undescribed sporozoan pathogen, was responsible for two mass mortalities in the 1984 cohort, in 1984 and in 1986, and eventually resulted in the extinction of this cohort. Anecdotal reports indicate that outbreaks of A. planci are increasing in frequency and severity. According to Fijian reef fishermen, the starfish were low to moderate in abundance in the Suva area from the 1920s to the 1960s. A progressive build up occurred on some reefs in 1963–67 leading to a major outbreak episode from 1967–1971. The outbreaks were in a chronic phase between 1977–1989. Our findings demonstrate that there is no invariable pattern or process involved in the population dynamics of A. planci and that a single explanation of the A. planci phenomenon is therefore unlikely.     

Population genetic studies of the crown-of-thorns starfish,Acanthaster planci (L.), in the Great Barrier Reef region

Seven populations of the crown-of-thorns starfish, Acanthaster planci, were compared genetically using starch gel electrophoresis in order to investigate the extent of genetic exchange throughout the Great Barrier Reef (GBR) region. These populations extended from Lizard Island in the north to One Tree Island in the south, a distance of approximately 1300 km. Thirteen of 36 enzymes assayed were genetically interpretable, and 10 (77%) of these were polymorphic. Mean heterozygosity over all loci was 0.225. An analysis of the gene frequency heterogeneity between the populations using Wright's F _ST statistic gave an overall F _ST of 0.019. The mean unbiased value of Nei's genetic distance between the populations was 0.009. These values indicate a homogeneous genetic composition throughout the range, and are consistent with the hypothesis that gene flow between these populations is high, and that A. planci throughout the GBR region are members of a single, effectively panmictic population. Within this group, the Green Island population was most distinct genetically because of differences in allele frequencies at the MDH-1 locus. Although there is no rigorous method for determining the selective basis for such differences, it is argued that the differences observed in the Green Island population were the result of selection. The basis for selective differences was possibly food availability since, at the time of sampling, the Green Island A. planci were the remnants of a large, high-density population that caused extensive coral mortality, and suffered severe population decline as food became scarce. These findings are consistent with observations of a relatively ordered sequence of outbreaks from north to south along the GBR, suggesting that all outbreaks but the first are secondary. Control measures, both on the GBR and elsewhere, have been unsuccessful except on a very small scale. Unless a vulnerable part of the A. planci life cycle can be identified, it would seem that the greatest chance for successful control would be to identify and control the causes of the primary population outbreak.     

Lipolytic enzymes of the digestive organs of the crown-of-thorns starfish (Acanthaster planci): comparison of the stomach and pyloric caeca

1. Stomach and pyloric caeca homogenates from the crown-of-thorns starfish hydrolysed p-nitrophenyl esters, alpha-naphthyl esters, cholesteryl oleate and tributyrin. The pyloric caeca contained the highest activities. 2. The p-nitrophenyl acetate hydrolytic activity eluted at 0.23 M NaCl on ion exchange chromatography while the p-nitrophenyl palmitate hydrolytic activity eluted between 0.2 and 1.0 M NaCl. 3. Polyacrylamide gel zymograms for alpha-naphthyl acetate hydrolytic activity revealed one major band and several minor bands of activity for both tissues. 4. Isoelectric focusing zymograms revealed one major band with a pI = 4.2 for both tissues, with an additional band at pI = 3.5 for pyloric caeca. 5. The pyloric caeca contained twice as much lipid as the stomach. Lipid extracts contained mixtures of steroids and steroid-esters; a cholesterol-like sterol was tentatively identified.     

Factors affecting the behaviour of crown-of-thorns starfish (Acanthaster planci L.) on the Great Barrier Reef:: 1: Patterns of activity

The feeding, moving and cryptic behaviours of 5749 crown-of-thorns starfish, Acanthaster planci (L.), were studied on 15 reefs of the Great Barrier Reef between June 1986 and December 1987. Log-linear analyses of field data showed that these behaviours were influenced by complex interactions between a number of important physical and biological factors including the size of starfish, their depth and physical condition, time of day, and substratum type. For most of these factors, the patterns of behaviour were shown to be consistent across reefs. Irrespective of their size, starfish spent on average about 45% of their time feeding. However, there were strong diurnal effects with smaller starfish (<20 cm) strongly favouring nocturnal feeding. For larger starfish (>40 cm) this pattern was reversed, though the diurnal effects were not as strong. Diurnal variation was greater at shallower depths (<3 m). Larger starfish spent more time moving (∼20%), particularly during the day, compared to smaller starfish (∼5%), with the latter moving mainly at night. Motion increased with depth for all starfish. The density and degree of aggregation of starfish had no effect on behaviour. The cryptic behaviour of starfish decreased with size, from ∼60% for small starfish to less than 10% for large starfish. For starfish <30 cm in size, there were strong diurnal effects on cryptic behaviour, with smaller starfish being almost exclusively cryptic during the day. Cryptic behaviour was also influenced by the condition of starfish. Those in poor condition were 5 times more likely to be moving than those in good condition. Cryptic starfish were 10 times more likely to be in good condition than non-cryptic starfish. This may partly explain the relatively rapid breakdown in starfish aggregations which has been observed at the ends of outbreaks.     

The thermal tolerance of crown-of-thorns (Acanthaster planci) embryos and bipinnaria larvae: implications for spatial and temporal variation in adult populations

To understand the role of sea temperature on the population biology of the crown-of-thorns sea star Acanthaster planci, the thermal window for embryonic and larval development was investigated. In two experiments, the response of embryos and larvae across 12 temperatures from 19.4 to 36.5 °C was quantified as the percentage of individuals reaching cleavage stage embryos, blastula, gastrula, early-bipinnaria, late-bipinnaria larvae or abnormal. Measurements were made at 7 times up to 72 h post-fertilisation, with the morphometrics of larvae measured in the 72-h sample. Acanthaster planci developed at temperatures between 19.4 and 33.2 °C, with a thermal window for development to the late-bipinnaria stage between 25.6 and 31.6 °C. Development rate, normal development and larval size were optimal at 28.7 °C, with development rates remaining relatively constant up to 31.6 °C. Rates of abnormality increased steadily (early embryonic stages) above 28.7 °C and was 100 % at temperatures approaching 33 °C. These experiments provide a more detailed insight into the response of A. planci developmental stages to temperature. The present day distribution of the species in eastern Australia overlap with the optimal thermal window for development to the late-bipinnaria stage (≈25–32 °C), implying a role of temperature in controlling population distributions and abundances. Despite this, short- or long-term temperature increases may not be a major modulator of the crown-of-thorns recruitment success, population dynamics and distribution in the future as no significant change in development rates, larval survival and growth occurred within this thermal window. Therefore, moderate (1–2 °C) increases in sea temperatures caused by El Niño or near-future ocean warming may not drive an increase in developmental and settlement success. Indeed, without any acclimation to warmer temperatures expected under near-future warming (+2 to 4 °C), climate change could ultimately reduce larval survival due to elevated mortality above the optimal development temperature.     

基于全基因组的河北省小麦品种遗传多样性分析

丰富的遗传变异对于提高作物的环境适应性和遗传改良进度至关重要。小麦是重要的粮食作物,河北省作为我国第三大小麦产区,在保障国家粮食安全中占有重要地位。建国以来,河北省审定了大量小麦品种,然而有关其遗传基础的研究却相对缺乏。本研究以1949年至2012年的169份河北省小麦品种为材料,利用覆盖小麦全基因组的SSR标记分析了供试小麦品种的遗传多样性。结果表明,供试河北省小麦品种的3个染色体组中,以B染色体组具有最高的遗传多样性,A组最低;7个同源群中,以第5、4群具有最高的多样性水平,而第7群最低;在21条染色体上的遗传多样性变化较大,以4A、2D具有较高的多样性水平,1A染色体最低。从品种的更新换代角度看,自1949年以来,尽管品种的等位基因频率在下降,河北省小麦品种的多样性水平基本呈现上升趋势。在此基础上,根据遗传相似系数,供试品种可聚为5大类,聚类结果既反映出河北省小麦品种多样性水平的复杂多样,也反映出品种的地域性分布特征。     

Genetic diversity and phylogenetic analysis of blackbuck (Antilope cervicapra) in southern India

Blackbuck (Antilope cervicapra) is a threatened species endemic to the Indian subcontinent. Many populations of blackbuck are found in southern India. Populations of blackbuck are negatively affected in many places for various reasons, such as habitat destruction and poaching. Their range decreased sharply during the 20th century. There is very limited information available on the population dynamics of blackbuck in southern India. For the phylogenetic and genetic diversity analyses of blackbuck populations among different distribution ranges in southern India, we sequenced mt DNA of cytochrome b (Cyt b) for 120, cytochrome c oxidase subunit-1 (COI) for 137 and the control region (CR) for 137 fecal pellets from eleven different locations in southern India. We analyzed the genetic structure of three mitochondrial markers, the CR, Cyt b and the COI region, separately and in a combined dataset. The haplotype diversity and nucleotide diversity of CR were 0.969 and 0.047, respectively, and were higher than those of Cyt b and COI. A Bayesian phylogeny and an MJ network based on the CR and combined dataset (105 sequences) signified several distinct haplotype clusters within blackbuck, whereas no clusters were identified with the Cyt b and COI phylogenetic analyses. The analysis of molecular variance of the combined data set revealed 52.46% genetic variation within the population. Mismatch distribution analysis revealed that blackbuck populations underwent complex changes with analysis of the combined dataset in each population and analysis of each marker separately in the overall population. The results provide evidence that blackbuck in different geographic locations has a distinct population structure due to habitat fragmentation after the formation of the Western and Eastern Ghats.

     

Genetic polymorphism of thyroxin-binding globulin (TBG) in the Pacific area.

Human plasma samples, radiolabeled with [125I]thyroxin, from the Asian, Pacific, and Australian area have been subjected to isoelectric focusing to reveal genetic variation in thyroxin-binding globulin (TBG). A genetically determined electrophoretic slow variant, TBG S, indistinguishable from the variant found in black Africans, has been observed with a frequency of 1%-10% in all Melanesian and Polynesian populations studied. The TBG S variant is present also with low frequency in Micronesians and in some Indonesian populations. However, East Asians, Indians, and Australian Aborigines were found to be monomorphic.     

A new snailfish of the genus Careproctus (Cottoidei: Liparidae) from the Pacific coast of southern Japan

Ichthyological Research - A new snailfish, Careproctus tomiyamai, is described on the basis of four specimens collected from Suruga Bay, Tosa Bay, and the Hyuga-nada Sea, southern Japan...     

基于Cyt b基因序列分析的松毛虫种群遗传结构研究

为了揭示松毛虫种群的遗传结构,采用DNA序列测定的方法测定了松毛虫不同种群的线粒体细胞色素b (Cyt b)基因的部分序列,并利用分子生物学软件分析其核苷酸组成、转换和颠换、氨基酸组成、遗传距离及亲缘关系。结果显示:在获得的Cyt b 基因387bp的序列中碱基A,T,C,G平均含量分别为40.1%、33.5%、9.5%、16.9%,A+T含量明显高于G+C含量表现出强烈的A、T偏向性,密码子第3位点的A+T含量高达86.5%,这种偏向性在种群间无明显差异。碱基替换主要发生在密码子第三位,转换大于颠换,且种群内替换高于种群间。该序列片段中共有39个核甘酸位点发生变异,遗传距离为0.000-0.100,显示出较小的遗传变异。蛋白质氨基酸由除谷氨酸以外的19种氨基酸组成。聚类分析结果表明马尾松毛虫和油松毛虫亚种遗传距离较近,种群间的遗传分化与生态环境有关。     

Genetic diversity and population structure of spottedtail goby (Synechogobius ommaturus) based on AFLP analysis

Larval dispersal may have an important impact on genetic structure of benthic fishes. To examine population genetic structure of spottedtail goby Synechogobius ommaturus, samples from five different locations of China and Kunsan population in Korea were analyzed by using amplified fragment length polymorphism (AFLP) technology. A total of 253 bands were identified from 91 individuals by 5 primer combinations and the percentage of polymorphic bands was 43.87%. The average gene diversity was 0.0794 ± 0.1470 and Shannon’s information index was 0.1279 ± 0.2138. The pairwise F_st values ranged from 0.022 to 0.201. The results of AMOVA analysis indicated that 90.54% of the genetic variation contained within populations and 9.46% occurred among populations. The gene flow estimates (Nm) demonstrated that different gene flow existed among populations from 0.994 to 11.114. No significant genealogical branches or clusters were recognized on the UPGMA tree. The results support the hypothesis that larval dispersal ability can be responsible for the genetic diversity and population structuring.     

Genetic diversity and structure of the endangered lady's slipper orchid Cypripedium japonicum Thunb. (Orchidaceae) in Japan

Cypripedium japonicum Thunb. (Orchidaceae), once a common perennial herb, is now designated as endangered throughout most of its distribution due to habitat destruction and fragmentation, and the impacts of horticultural collection. We investigated the genetic characteristics of this species for conservation purposes, using microsatellite markers to examine the genetic diversity and structure of 15 native and 5 ex situ populations in Japan. The results imply that although allelic variation is low in Japanese C. japonicum, sexual reproduction by seed, as well as clonal propagation, may occur in some populations. Both native and ex situ populations were found to be genetically differentiated, indicating that some populations may have experienced recent population declines, genetic fragmentation, or bottlenecks. The degree of genetic drift from the putative ancestral population, inferred through STRUCTURE analysis, was more pronounced in northern populations than in southern populations. Some of the ex situ conserved populations exhibited a low degree of differentiation from ancestral native populations. Our results imply that conservation of C. japonicum in Japan is best supported by maintaining individual populations and their unique genetic characteristics.