Allozyme evidence for the origin and diversification of Gossypium barbadense L.

Summary Gossypium barbadense L. is a commercially important cotton species of tropical South American origin presently grownin many regions of the world. The species is morphologically diverse, consisting of a wide range of wild (or feral), commensal, landrace, and highly improvedcommercial forms. We performed allozyme analysis on 153 accessions representing the spectrum of G. barbadense diversityto ascertain the geographic origin of the species, its patterns of diffusion subsequent to domestication, and to reveal infraspecific relationships. Levels ofgenetic variation in G. barbadense are moderate. Of 59 loci scored, 24 were polymorphic, with a mean number of alleles perlocus of 1.69 and an average panmictic heterozygosity of 0.062. Principal component analysis revealed geographic clustering of accessions into six relativelydiscrete regions. Gene frequencies at many loci are significantly heterogeneous among these regions, with an average G _STof 0.272. Northwestern South America contains the greatest genetic variability; we suggest that this region is the ancestral home of the species. The data indicate separate diffusion pathways from this region into Argentina-Paraguay and into eastern and northern South America east of the Andes. Caribbean Island and Central American forms appear to be derived from the latter. These diffusion pathways are in accordance with morphological evidence and historical record. In contrast to expectations based on geographic proximity, Pacific Island forms have their closest affinity to accessions from eastern South America. Advanced cultivated stocks seem largely derived from western Andean material, but also contain introgressed G. hirsutum germ plasm. Introgression was relatively high (22%–50% of accessions) in commercial stocks and in forms from Argentina-Paraguay and various Pacific Islands, but was conspicuously low or absent in material from Central America and the Caribbean, where commensal and commercial forms of both species are sympatric.     

Molecular phylogeny of Eastern Pacific porcelain crabs, genera Petrolisthes and Pachycheles, based on the mtDNA 16S rDNA sequence: phylogeographic and systematic implications

Porcelain crabs, genera Petrolisthes and Pachycheles, are diverse and abundant members of the eastern Pacific near-shore decapod crustacean community. Morphology-based taxonomic analyses of these crabs have determined groupings of affiliated species, but phylogenetic relationships remain unknown. We used sequence data from the mitochondrial 16S rRNA gene of 46 species of eastern Pacific porcelain crabs to perform phylogenetic analyses by distance and parsimony methods. Our results are used to compare the taxonomic significance of morphological and molecular characters, to examine sequence divergence rates of crab 16S rRNA genes, and to analyze the phylogeographic history of these crabs. Our phylogenetic trees indicate that the genus Petrolisthes is divided into two main clades, reflecting morphological features. One clade contains primarily tropical species, and the other contains species from throughout the eastern Pacific, as well as species in the genera Allopetrolisthes and Liopetrolisthes. Phylogenetic trees of Pachycheles suggest an antitropical distribution; north and south temperate species form one clade and tropical species form a second clade. Sequence divergence rates of the 16S rRNA gene from three pairs of geminate species can be used to date divergence times, and we discuss porcelain crab phylogeographic patterns in relation to paleogeographic events.     

A molecular phylogenetic framework for the subfamily Ocenebrinae (Gastropoda,Muricidae)

The Ocenebrinae is a subfamily of marine predatory gastropods known as oyster and mussel drills. Their current phylogenetic framework is traditionally based on shell and radular characters, but a consensus on relationships among genera is still lacking. We investigated the molecular phylogeny of Ocenebrinae using 50 species and DNA data from one nuclear (28S) and two mitochondrial (COI and 16S) genes, the largest data set so far assembled for this subfamily. We found support for the monophyly of the Ocenebrinae, and species were divided into four major lineages. Within groups, genera had similar geographic distributions, suggesting that except in a few cases, species diversification within clades occurred without range expansions. We discuss the phylogenetic distribution of a labral tooth and a sealed siphonal canal, two characteristic ocenebrine features. We also show that Ocinebrina species in the north‐eastern Pacific are not monophyletic with north‐eastern Atlantic and Mediterranean species, and that the Ocinebrina edwardsii species complex belongs to Ocenebra.     

Chromosome painting supports lack of homology among sex chromosomes in Oncorhynchus, Salmo, and Salvelinus (Salmonidae)

The sex chromosome pair has been identified previously as the largest submetacentric pair in the genome in several species of the genus Salvelinus (eastern trouts and chars) including S. namaycush (lake trout) and as a large subtelocentric/acrocentric pair in several species of the genus Oncorhynchus (Pacific trouts and salmon). Sex chromosomes have not been identified in Salmo (Atlantic salmon and brown trout). Two paint probes, one specific for the short arm (Yp) and the other for the long arm (Yq) of the sex chromosome pair in Salvelinus namaycush were hybridized to chromosomes of Oncorhynchus mykiss (rainbow trout) and O. tshawytscha (chinook salmon) and Salmo salar (Atlantic salmon) and S. trutta (brown trout). The two probes hybridized to two different autosomal pairs in each of the Oncorhynchus species, supporting lack of homology between the sex chromosomes in the two genera. The Yp probe hybridized to interstitial regions on two different chromosome pairs in S. salar and one pair in S. trutta. The Yq probe hybridized to a different pair in both species.     

Cryptic diversity,biogeography and genetic variation in Northeast Pacific species of <Emphasis Type="Italic">Porphyra</Emphasis> sensu lato (Bangiales,Rhodophyta)

We sequenced the chloroplast rubisco large subunit (rbcL) gene in 236 samples of Porphyra sensu lato from the northeast Pacific. Comparisons of sequences within the study area as well as comparisons with published sequences revealed up to five cryptic species among the 22 named species: a species closely related to Porphyra abbottiae, a species previously identified as P. pseudolinearis, a species closely related to P. pseudolanceolata and previously identified as that species, a previously unknown species from the eastern Aleutian Islands, and a species closely related to P. schizophylla and previously identified as that species. All of these previously unrecognized species had high bootstrap values separating them from the other species. In addition, our wide geographic sampling allowed us to extend, curtail or clarify the geographic ranges of a number of the species. We also provide published sequences for P. gardneri and P. smithii for the first time. We compared amount of sequence divergence within species grouped on the basis of sexuality (monoecious, sectored into separate male and female “halves”, or dioecious), habitat (high, mid, or low intertidal/subtidal), and seasonality (winter, spring, or summer) using Tukey’s HSD t test, but we observed no significant differences between species grouped in this manner. Different species showed different levels of genetic variation in the rbcL gene apparently unrelated to these traits. Also, we observed no differences in the patterns of genetic variation in a species based on whether the specimens were collected from outside or from within the region covered by ice during Pleistocene glaciations.     

New species in the rheophilous genus Nicsmirnovius Chiambeng & Dumont, 1999 (Branchiopoda: Anomopoda: Chydoridae) and reassignment of Alona eximia Kiser, 1948 and Alonella fitzpatricki Chien, 1970

A morphological comparison of specimens previously assigned to Alona eximia Kiser, 1948 from tropical Africa, Eastern Asia and the Americas shows that this species-group shares a number of morphological characters on the postabdomen, head pores, first antenna and second and fourth limb that separate them from Alona Baird, 1843 but unite them with Nicsmirnovius Chiambeng & Dumont, 1999. Alonella fitzpatricki Chien, 1970, formerly believed to be a junior synonym of A. eximia, is separated from the latter and assigned to the genus Nicsmirnovius. Two new taxa, from Africa and the Island of Socotra (Yemen) are added to the genus. The relationship between the specialised habitat of these chydorids and their morphology is discussed. The geographic range of all known populations is figured and a key to species is presented.     

Geographic distribution of the bathypelagic genus paraeuchaeta (Copepoda,Calanoida)

The geographic distribution of the bathypelagic calanoid genus Paraeuchaeta was investigated by examining midwater trawl and plankton net samples collected mostly from depths exceeding 1000 m throughout the world's oceans. Of the 81 species referred to Paraeuchaeta, the geographic ranges of about 50 species could be defined with reasonable certainty. Contrary to early authors, the number of species having a worldwide distribution was surprisingly small (12 species or 15% of the 81 species of the genus) as compared to common species endemic to various geographic regions (34 species or 42% of the total of 81). Almost twice as many species were found in the Indo-Pacific Ocean as in either the Atlantic or the Southern Ocean. Faunistically, the northern Atlantic, mid-Atlantic, northern Pacific, East Pacific, Indo-West Pacific, and Southern Ocean were distinct in terms of endemic species. A number of species were found to be endemic to highly productive areas, where they were usually very abundant. Rare species, on the other hand, were generally found to be widely distributed, although some were too rare for their range to be determined with certainty. To explain these findings, the following hypothesis is proposed: Bathypelagic calanoids endemic to and abundant in eutrophic areas are those adapted to eutrophic conditions of their habitats and therefore cannot expand their ranges into contiguous oligotrophic waters even if the other environmental conditions are favorable. Other species, on the other hand, generally have extensive geographic ranges because of their survival ability in widely expanding oligotrophic conditions and the absence of physicochemical barriers at bathypelagic depths of the world's oceans.     

Taxonomic status of three nominal species of Indo-Pacific symphurine tonguefishes (Symphurus: Cynoglossidae: Pleuronectiformes)

The taxonomic status of three rarely captured, nominal species of Indo-Pacific symphurine tonguefishes,Symphurus trifasciatus (Alcock, 1894),S. microrhynchus (Weber, 1913), andS. holothuriae Chabanaud, 1948, is resolved.Symphurus microrhynchus, previously known only from three specimens, is redescribed based on 12 specimens.Symphurus holothuriae, previously reported only from the holotype, is a junior subjective synonym ofS. microrhynchus. Symphurus trifasciatus is redescribed based on six specimens, including the lectotype designated in this study.Symphurus microrhynchus is distinguished from congeners by a combination of meristic features, head and opercle shape, dorsalfin position, and features of its pigmentation. The species occurs in relatively shallow tropical waters from Zanzibar through French Polynesia (the only reported occurrence of a shallow-waterSymphurus from a locality on the Pacific Plate), including Indonesia, Papua New Guinea, Vietnam, and northwestern Australia.Symphurus trifasciatus, known from deep waters along both coasts of the Indian subcontinent and adjacent waters, has an overall similarity in body shape and meristic features reminiscent of those inS. microrhynchus, but differs notably in having a longer and wider head, a distinctive opercle shape, number of scale rows on the head, and pigmentation pattern.     

Molecular data illuminate cryptic nudibranch species: the evolution of the Scyllaeidae (Nudibranchia: Dendronotina) with a revision of Notobryon

Scyllaeidae represents a small clade of dendronotoid nudibranchs. Notobryon wardi Odhner, 1936, has been reported to occur in tropical oceans from the Indo‐Pacific and eastern Pacific to temperate South Africa. The systematics of Notobryon has not been reviewed using modern systematic tools. Here, specimens of Notobryon were examined from the eastern Pacific, the Indo‐Pacific, and from temperate South Africa. Additionally, representatives of Scyllaea and Crosslandia were studied. Scyllaeidae was found to be monophyletic. Notobryon was also found to be monophyletic and is the sister group to Crosslandia plus Scyllaea. The molecular data also clearly indicate that within Notobryon, at least three distinct species are present, two of which are here described. Genetic distance data indicate that eastern Pacific and South African exemplars are 10–23% divergent from Indo‐Pacific exemplars of Notobryon wardi. Scyllaea pelagica has been regarded as a single, circumtropical species. Our molecular studies clearly indicate that the Atlantic and Indo‐Pacific populations are distinct and we resurrect Scyllaea fulva Quoy & Gaimard, 1824 for the Indo‐Pacific species. Our morphological studies clearly corroborate our molecular findings and differences in morphology distinguish closely related species. Different species clearly have distinct penial morphology. These studies clearly reinforce the view that eastern Pacific, Indo‐Pacific, and temperate biotas consist largely of distinct faunas, with only a minor degree of faunal overlap. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 311–336.     

Genomic Approaches Reveal Unexpected Genetic Divergence Within Ciona intestinalis

The invertebrate chordate Ciona intestinalis is a widely used model organism in biological research. Individuals from waters ranging from arctic to temperate are morphologically almost indistinguishable. However, we found significant differences in whole genomic DNA sequence between northern European and Pacific C. intestinalis. Intronic and transposon sequences often appear unrelated between these geographic origins and amino acid substitutions in protein coding sequences indicate a divergence time in excess of 20 MYA. This finding suggests the existence of two cryptic species within the present C. intestinalis species. We found five marker loci which distinguish the two genetic forms by PCR. This analysis revealed that specimens from Naples, Italy, have the Pacific-type genome, perhaps due to human-mediated marine transport of species. Despite major genomic divergence, the two forms could be hybridized in the laboratory. [Reviewing Editor: Dr. Martin Kreitman]     

Redescription ofaulopus bajacali parin & kotlyar, 1984, comments on its relationships and new distribution records

Aulopus bajacali, described from the eastern Pacific Ocean from a single specimen, is redescribed. It is now known from over 400 specimens. It is the only Pacific species ofAulopus belonging with the Atlantic species group ofA. nanae, A. filamentosus, andA. cadenati. It shares a short dorsal-fin base and some color pattern characters with this group. New distribution records from Ecuador and the Galapagos Islands extend its range; it is now known from mid-Baja California (25°N) to about 3°S in the eastern central Pacific.     

Genetic diversity,distributional barriers and rafting continents — more thoughts on the evolution of mangroves

Without continental drift, the diversity and distribution of many species, including mangrove plants, would be very different today. First, there would be fewer pantropic genera and many more endemics. Second, their characteristics would not be as common and widespread as some are today. Continental drift has brought about the massive mixing and dispersal of genes in geologically recent times, greatly enhancing the evolutionary process; particularly for flowering plants — the angiosperms, which evolved during the period.Mangrove plants are comprised of approximately 70 species from 20 quite different angiosperm families. Most taxa are characterized by special physiological abilities and structural forms, enabling them to live in both seasonally fluctuating saline conditions, and water-saturated soils. Their occurrence is mostly tropical, perhaps because of harsh physiological conditions of intertidal habitats; but distributions of specific taxa do not fully concur with the idea of a completely tropical evolution, at least for some important species.At least one genus of mangrove tree, Avicennia, occurs around the world, chiefly in tropical estuarine habitats, although they also range into temperate latitudes, especially in the south. Around the world, there are no more than ten species of Avicennia recognised today, but their diagnostic determinants were inadequate prior to recent studies using both numerical analyses of morphological parameters and isozymes. Such analyses significantly reduced the number of apparent species, notably around Australia, and provided a basis for the revision of distributional records throughout the Indo West Pacific region. One species, A. marina, was found to be widespread and morphologically variable with genes divided into characteristic groupings of at least three geographic areas in the region. Based on these findings, there are several novel inferences to be made regarding the evolution of this genus. A western Gondwanan origin is proposed, with subsequent radiation of several taxa facilitated via the tectonic dispersal of southern continental fragments.     

Growth and mortality of bigeye tuna <Emphasis Type="Italic">Thunnus obesus</Emphasis> (Scombridae) in the eastern and central tropical Pacific Ocean

Biological parameters such as age, growth and age (or size) at maturity are vital for stock assessment and management. Aging is essential in yielding such information. However, limited aging studies have been conducted for large tropical pelagic species in the eastern and central tropical Pacific Ocean. The objective of this study is to conduct a length frequency analysis for estimating growth and mortality of bigeye tuna in the eastern and central tropical Pacific Ocean using samples from the Chinese longline fishery during February to November 2006. The von Bertalanffy growth parameters of asymptotic fork length L _∞ and growth coefficient k were estimated at L _∞ = 207.4 cm fork length, k = 0.23 year^-1, and theoretical age at zero length t ₀ = −0.40 year. The total mortality rate (Z) was estimated to be 0.60; the fishing mortality rate (F) and the natural mortality rate (M) were 0.25 year^-1 and 0.35 year^-1, respectively. The exploitation rate (E) was 0.16. This study provides the estimates of growth and mortality rate for bigeye tuna in the eastern and central tropical Pacific Ocean, which can be used as biological input parameters in further stock evaluations in this region. However, age analysis, further validation of the age composition and stock structure are needed for future studies.     

Generic delimitation and biogeography of Maianthemum and Smilacina (Ruscaceae sensu lato): preliminary results based on partial 3′ matK gene and trnK 3′ intron sequences of cpDNA

The controversy over generic delimitation between Maianthemum and Smilacina has been unresolved for almost two centuries. Distributions of the two genera in the Northern Hemisphere also provide an excellent opportunity to further understand the disjunct distribution patterns of the North Temperate Flora. To test the generic delimitation and to investigate biogeographic patterns, we sequenced the partial 3′ matK gene and trnK 3′ intron of chloroplast DNA for 38 accessions, representing three species of Maianthemum, seven species of Smilacina, and four outgroup taxa. Maximum parsimony and neighbor-joining trees showed reciprocal monophyly of the two genera with very weak bootstrap support for each genus. Within each genus, relationships among species were poorly resolved. Despite its low resolution, this study shows that eastern Asian species of Smilacina and Maianthemum are generally more closely related to eastern North American taxa than to western ones. More detailed sampling of Smilacina from different geographic regions, especially from the two centers of diversity (southeastern Asia and Mexico/Central America), and additional sequences from cpDNA, as well as from nuclear DNA, are needed to test the reciprocal monophyly of the two genera and also to understand current distributions of disjunct taxa.     

柔鱼科近缘种茎柔鱼与鸢乌贼营养生态位及相互关系

同域近缘种由于进化选择的压力,会形成不同的行为适应策略。研究同域近缘种生态位格局,有助于理解近缘物种的竞争和共存机制,是深入了解种群动态变化的基础性问题。选取东太平洋赤道海域的柔鱼科头足类近缘种茎柔鱼和鸢乌贼为研究对象,利用生物地球化学示踪物(稳定同位素和脂肪酸)分析两种头足类的营养生态位及相互关系。结果显示,茎柔鱼和鸢乌贼肌肉的部分必需脂肪酸(C18∶2n6、C20∶2n6、C20∶3n3、C20∶4n6和C20∶5n3)含量存在差异,说明二者食物来源不同,但其碳、氮稳定同位素比值无显著差异,可能是因为相同个体大小的茎柔鱼和鸢乌贼营养级相近,且摄食空间相似。这些结果在营养生态位的分析结果中也得到了验证,稳定同位素营养生态位的重叠程度高于脂肪酸营养生态位,表明脂肪酸组成更能体现同域近缘种的食性差异。本研究可加深对头足类进化过程中摄食行为适应机制的理解,并为评估同域近缘种的营养生态位关系提供有益参考。     

Differences in oscillatory whistles produced by spinner (Stenella longirostris) and pantropical spotted (Stenella attenuata) dolphins

Acoustic recordings of two closely related species, spinner dolphin (Stenella longirostris) and pantropical spotted dolphin (Stenella attenuata), were investigated from four different geographic locations: two in the Central Tropical Pacific, one in the Eastern Tropical Pacific and one in the Indian Ocean. The two delphinid species occur in tropical and warm temperate waters, with overlapping ranges. They produce very similar vocalizations, but at the same time their calls exhibit a certain degree of intraspecific variation among different geographic locations as has been observed in other delphinid species. Oscillatory whistles (whistles with at least two oscillations in their frequency contours) were identified and manually extracted from the recordings. Whistles with four or more maxima (oscillations) occurred only in spinner dolphins and they were present in all geographic regions investigated. In addition, the oscillatory whistles with two and three maxima were significantly more frequent in spinner than in spotted dolphins. The differences in oscillatory whistles for these two species seem to be consistent across study areas and therefore, could be used in addition to other whistle features to help distinguish between them.     

Leptodiscaceans (Noctilucales, Dinophyceae) from the Pacific Ocean: First records of Petalodinium and Leptodiscus beyond the Mediterranean Sea

Records of dinoflagellates of the family Leptodiscaceae (Noctilucales) from the Kuroshio Current, Philippine, Celebes, Sulu, South China Seas and the western and central Equatorial Pacific Ocean are described. Scaphodinium mirabile was the most common leptodiscacean. Two specimens that differed from the type species of Scaphodinium were found: one specimen showed a highly bifurcate proximal extremity and another showed two dissimilar proboscides from the distal extremity. Another unidentified leptodiscacean showed an arrowhead-shaped contour with the margins folded. Six specimens of Petalodinium porcelio were found, being the first record beyond the Mediterranean-Black Seas. Six specimens were tentatively assigned to the genus Leptodiscus, being the first record beyond the western Mediterranean Sea. The folded specimens that ranged from 90 to 120 μm in diameter and with a prominent flagellum were tentatively considered to be young specimens of Leptodiscus. The abundance of the leptodiscaceans is underestimated in the world's oceans.     

Observations on the morphology of some North American nemertines with consequent taxonomic changes and a reassessment of the architectonics of the phylum

A majority of the nemertine species from the western North Atlantic were originally described from life in the nineteenth century. Many of these were established by A. E. Verrill who had ‘an eye for species’ no matter which phylum he was working with, and thus when living nemertines which he described are encountered, they can usually be recognized. The morphology of most of these species has never been reported; some may prove to be species described earlier from the eastern North Atlantic. Morphological observations on the nemertine species from the North East coast of the Pacific are inadequate and have prevented satisfactory comparison with species from Japan and eastern Russia. The morphology of some species collected in the Gulf of Maine and from Cape Cod, as well as a re-examination of some of the slides of type specimens of species from the west coast of North America, indicates that their generic placement must be re-examined. The architectonic plan of the heteronemertines postulated over 100 years ago can not be substantiated and is redescribed. Three new heteronemertean genera are described: Tenuilineus gen.n. Parvicirrus gen.n., Tarrhomyos gen.n.     

Trichome morphology provides phylogenetically informative characters for Tremandra, Platytheca and Tetratheca (former Tremandraceae)

Summary Trichomes of Tremandra R.Br. ex DC., Platytheca Steetz and Tetratheca Sm. (Elaeocarpaceae, former Tremandraceae), together with two outgroup species of Elaeocarpus L., are illustrated using scanning electron microscopy, and their distribution on various plant organs is documented. Various trichomes types were identified that relate taxa: simple hairs, stellate hairs, short glandular trichomes, long glandular trichomes, and three forms of tubercules. Both outgroup and ingroup taxa have simple hairs. Stellate hairs are confirmed as unique to Tremandra. Prominent and sculptured multicelled tubercules, some bearing a stout hair, are characteristic of Platytheca. Smaller multicelled tubercules occur in both Platytheca and Tetratheca, except for the Western Australian taxon Te. filiformis Benth. (possibly plesiomorphic). Unicellular tubercules (papilla) characterise two species of Tetratheca. Short glandular trichomes, usually found on the ovary, also occur in both of these genera but not in all species (possibly secondary losses), while long glandular trichomes, usually on stems and leaves, occur only in some groups of Tetratheca. Within Tetratheca, Western Australian taxa that have five-merous flowers fall into three ‘groups’: seven species (together with one from South Australia) that have short glandular trichomes but no long glandular trichomes; six species that have long glandular trichomes but no short glandular trichomes; and four species that have both trichome types. All other species of Tetratheca have four-merous flowers and form two ‘groups’: 12 eastern species (including one from South Australia) that have both short glandular trichomes and long glandular trichomes; 4 western species and six eastern species that lack short glandular trichomes. On the basis of these characters, a phylogenetic hypothesis for the three genera is presented.