Genetic patterns and conservation of the Scarlet Macaw (<Emphasis Type="Italic">Ara macao</Emphasis>) in Costa Rica

Once widely distributed throughout the lowland forests of Costa Rica, scarlet macaws (Ara macao) have been reduced to two major, geographically separated, populations along the Pacific slope. Past demographic declines raise conservation concerns regarding the detrimental effects of population fragmentation. This investigation aimed to evaluate the current status of scarlet macaws along the Pacific slope by examining levels of genetic variation and patterns of genetic structure within and among remnant populations. Statistical analyses using multilocus genotypes revealed strong differentiation between Central and South Pacific populations, suggesting local geographic barriers have historically restricted gene flow between these localities. High genetic diversity suggests neither population suffers from genetic erosion, likely resulting from relatively large population sizes and high dispersal capacity and longevity. However, evidence of disequilibrium within the Central Pacific population infers anthropogenic threats have disrupted natural population dynamics. These results advocate on focusing available resources on habitat restoration and nest protection, as a means to assist in reestablishing demographic stability and maintain the genetic health of wild scarlet macaws in Costa Rica.     

Evidence of local short‐distance spawning migration of tropical freshwater eels,and implications for the evolution of freshwater eel migration

Freshwater eels have fascinated biologists for centuries due to the spectacular long‐distance migrations between the eels’ freshwater habitats and their spawning areas far out in the ocean and the mysteries of their ecology. The spawning areas of Atlantic eels and Japanese eel were located far offshore in the Atlantic Ocean and the Pacific Ocean, respectively, and their reproduction took place thousands of kilometers away from their growth habitats. Phylogenetic studies have revealed that freshwater eels originated in the Indonesian region. However, remarkably little is known about the life histories of tropical freshwater eels despite the fact that tropical eels are key to understanding the nature of primitive forms of catadromous migration. This study found spawning‐condition tropical freshwater eels in Lake Poso, central Sulawesi, Indonesia, with considerably high gonadosomatic index values and with histologically fully developed gonads. This study provides the first evidence that under certain conditions, freshwater eels have conditions that are immediately able to spawn even in river downstream. The results suggest that, in contrast to the migrations made by the Atlantic and Japanese eels, freshwater eels originally migrated only short distances of <100 kilometers to local spawning areas adjacent to their freshwater growth habitats. Ancestral eels most likely underwent a catadromous migration from local short‐distance movements in tropical coastal waters to the long‐distance migrations characteristic of present‐day temperate eels, which has been well established as occurring in subtropical gyres in both hemispheres.     

THE EVOLUTIONARY GENETIC STATUS OF ICELANDIC EELS

The Iceland population of Anguilla eels contains an elevated frequency of fish with vertebral numbers lower than those typical of European localities. Several distinct hypotheses have been advanced to account for these morphologically atypical fish: for example, they could represent (1) genetically “pure” American expatriates, (2) genetically “pure” European types with ontogenetic abnormalities, or (3) hybrids between American and European forms. Here we critically test these and other possibilities by examining the joint distributions of allozyme markers, mitochondrial DNA markers, and vertebral numbers in Icelandic eels. The particular patterns of association among the genetic and morphological traits demonstrate that the Iceland population includes, in low frequency, the products of hybridization between American and European eels. Approximately 2–4% of the gene pool in the Iceland eel population is derived from American eel ancestry. This hybrid zone is highly unusual in the biological world, because the mating events in catadromous eels presumably take place thousands of kilometers from where the hybrids are observed as maturing juveniles. The molecular data, in conjunction with the geographic distributions, strongly suggest that the differences in migrational behavior and morphology between American and European eels include an important additive genetic component. Evolutionary hypotheses are advanced to account for the original separation of North Atlantic eels into American and European populations, and for the presence of hybrids in Iceland.     

Phylogeography of Anguilla marmorata (Teleostei: Anguilliformes) from the eastern Caroline Islands

Recent analyses of the tropical giant mottled eel Anguilla marmorata have suggested four to six populations within its Indo-Pacific distribution, including one represented by specimens from Guam, and that the population on Guam includes eels occurring in the eastern Caroline Islands based on morphological similarities. To test this hypothesis, sequences of the entire mitochondrial control region (mtCR) were obtained for 39 eels from Kosrae and Pohnpei, and compared to 267 previously sequenced haplotypes from across the Indo-Pacific Ocean. Results support recognition of two lineages distinctive for the eastern Caroline Islands and Guam, and the likelihood of an additional spawning area in the Indo-Pacific Ocean.     

Deep-ocean origin of the freshwater eels

Of more than 800 species of eels of the order Anguilliformes, only freshwater eels (genus Anguilla with 16 species plus three subspecies) spend most of their lives in freshwater during their catadromous life cycle. Nevertheless, because their spawning areas are located offshore in the open ocean, they migrate back to their specific breeding places in the ocean, often located thousands of kilometres away. The evolutionary origin of such enigmatic behaviour, however, remains elusive because of the uncertain phylogenetic position of freshwater eels within the principally marine anguilliforms. Here, we show strong evidence for a deep oceanic origin of the freshwater eels, based on the phylogenetic analysis of whole mitochondrial genome sequences from 56 species representing all of the 19 anguilliform families. The freshwater eels occupy an apical position within the anguilliforms, forming a highly supported monophyletic group with various oceanic midwater eel species. Moreover, reconstruction of the growth habitats on the resulting tree unequivocally indicates an origination of the freshwater eels from the midwater of the deep ocean. This shows significant concordance with the recent collection of mature adults of the Japanese eel in the upper midwater of the Pacific, suggesting that they have retained their evolutionary origin as a behavioural trait in their spawning areas.     

Fecundity of the tropical catadromous eels <Emphasis Type="Italic">Anguilla bicolor bicolor</Emphasis>, <Emphasis Type="Italic">A. bengalensis bengalensis</Emphasis> and <Emphasis Type="Italic">A. marmorata</Emphasis>

Maturation is one of the most important ontogenetic transitions in an individual’s life. However, the reproductive ecology of the tropical anguillid eel genus Anguilla at the onset of oceanic spawning migration is poorly understood. To understand the reproductive ecology, the fecundity of the tropical eels Anguilla bicolor bicolor, A. bengalensis bengalensis and A. marmorata was examined using advanced migrating silver eels (Stage IV and V). A close linear relationship was found between total length and fecundity in A. bengalensis bengalensis. The fecundities of A. bicolor bicolor (0.55 to 4.96 × 10⁶), A. bengalensis bengalensis (0.33–1.72 × 10⁶) and A. marmorata (0.99 × 10⁶) were within the range of those observed in temperate eels.     

RELATIONSHIPS BETWEEN INFERRED LEVELS OF GENE FLOW AND GEOGRAPHIC DISTANCE IN A PHILOPATRIC CORAL,BALANOPHYLLIA ELEGANS

When the dispersal capability of a species is considerably less than its geographic range, genetic differences between populations should increase with the distance separating those populations. This pattern should be most evident in linearly distributed species. The sessile solitary cup coral Balanophyllia elegans lives along nearly the entire Pacific coast of North America, yet its crawling larvae usually settle within 40 cm of their birthplace. In this paper, I document geographic patterns of allozyme differentiation within and among populations of B. elegans and estimate the proportion of observed geographic pattern attributable to gene flow between adjacent populations. Genetic subdivision among localities separated by up to 3000 km was high (F_ST = 0.283, SE = 0.038). Inferred gene flow between pairs of localities (, individuals per generation) correlated inversely with the geographic distance between those localities, consistent with the pattern expected for a species at equilibrium in which gene flow occurred exclusively between adjacent localities. Within localities, patches separated by 4 to 30 m were also significantly subdivided, but genetic differentiation between patches did not vary significantly with the distance separating them. Simulations revealed that the power to detect genetic pattern expected from gene flow between adjacent populations increased with both the number of loci used to infer gene flow and the heterozygosity of those loci. Simulations also verified that when geographic distance poorly approximated the number of steps between populations, reduced major-axis regression more accurately portrayed the structural relationship between gene flow and separation than did ordinary least-squares regression. Attenuation of gene flow with distance explained 15% of the between-locality pattern of genetic differentiation in B. elegans. The remaining variation appeared to be due to neither natural selection nor a recent rangewide recolonization. Loci from the northern sampled localities, however, had fewer alleles than those from the remainder of the range, suggesting these localities had been recolonized recently following Pleistocene cooling.     

Population structure and variability of Pacific herring (<Emphasis Type="Italic">Clupea pallasii</Emphasis>) in the White Sea,Barents and Kara Seas revealed by microsatellite DNA analyses

Pacific herring, Clupea pallasii, have recently colonised the northeast Atlantic and Arctic Oceans in the early Holocene. In a relatively short evolutionary time, the herring formed a community with a complex population structure. Previous genetic studies based on morphological, allozyme and mitochondrial DNA data have supported the existence of two herring subspecies from the White Sea and eastern Barents and Kara Seas (C. p. marisalbi and C. p. suworowi, respectively). However, the population structure of the White Sea herring has long been debated and remains controversial. The analyses of morphological and allozyme data have previously identified local spawning groups of herring in the White Sea, whereas mtDNA markers have not revealed any differentiation. We conducted one of the first studies of microsatellite variation for the purpose of investigating the genetic structure and relationship of Pacific herring among ten localities in the White Sea, the Barents Sea and the Kara Sea. Using classical genetic variance-based methods (hierarchical AMOVA, overall and pairwise F _ST comparisons), as well as the Bayesian clustering, we infer considerable genetic diversity and population structure in herring at ten microsatellite loci. Genetic differentiation was the most pronounced between the White Sea (C. p. marisalbi) versus the Barents and Kara seas (Chesha–Pechora herring, C. p. suworowi). While microsatellite variation in all C. pallasii was considerable, genetic diversity was significantly lower in C. p. suworowi, than in C. p. marisalbi. Also, tests of genetic differentiation were indicating significant differentiation within the White Sea herring between sympatric summer- and spring-spawning groups, in comparison with genetic homogeneity of the Chesha–Pechora herring.     

Genetic Analysis of the Populations of Japanese Anchovy (Engraulidae: Engraulis japonicus) Using Microsatellite DNA

We analyzed the population structure of the Japanese anchovy (Engraulis japonicus), a small pelagic fish, using 6 microsatellite DNA loci. The anchovy is known to have 2 separate spawning populations, one near northeastern Taiwan in the Pacific Ocean and the other near southwestern Taiwan in the Taiwan Strait. The planktonic larvae then drifted north to the feeding grounds in the East China Sea to advance in their life history. Three populations of the anchovy were analyzed, including 2 temporal population from the northeastern spawning ground (I-Lan 1999 and I-Lan 2000) and one population from the southwestern spawning ground (Peng-Hu 2000). The genetic variability of the 6 loci was high for all the populations. The average numbers of alleles per population ranged from 25.5 to 32.3, and the average observed heterozygosity ranged from 0.559 to 0.650. A significant population differentiation was found between geographic populations but not between the temporal populations. However, the level of geographic differentiation was weak, average FST 0.0088. The significant geographic population structure indicated that the populations of 2 spawning grounds belonged to separate stocks. Moreover, 16 of the 18 population-locus cases showed significant departure from Hardy-Weinberg equilibrium, implying that each spawning population in turn consisted of mixed native stocks. Finally, we posed 3 population models to be evaluated against the genetic data disclosed with the microsatellite markers.     

Present and past genetic connectivity of the Indo‐Pacific tropical eel Anguilla bicolor

Aim The objective of this study was to reveal the present population structure and infer the gene‐flow history of the Indo‐Pacific tropical eel Anguilla bicolor. Location The Indo‐Pacific region. Methods The entire mitochondrial control region sequence and the genotypes at six microsatellite loci were analysed for 234 specimens collected from eight representative localities where two subspecies have been historically designated. In order to infer the population structure, genetic differentiation estimates, analysis of molecular variance and gene‐tree reconstruction were performed. The history of migration events and population growth was assessed using neutrality tests based on allelic frequency spectrum, coalescent‐based estimation of gene flow and Bayesian demographic analysis using control region sequences. Results Population structure analysis showed genetic divergence between eels from the Indian and Pacific oceans (F_ST = 0.0174–0.0251, P < 0.05 for microsatellites; Φ_ST = 0.706, P < 0.001 for control region), while no significant variation was observed within each ocean. Two mitochondrial sublineages that do not coincide with geographical regions were found in the Indian Ocean clade of a gene tree. However, these two sublineages were not differentiated at the microsatellite markers. The estimation of mitochondrial gene‐flow history suggested allopatric isolation between the Indian and Pacific oceans, and a possible secondary contact within the Indian Ocean after an initial population splitting. Bayesian demographic history reconstruction and neutrality tests indicated population growth in each ocean after the Indo‐Pacific divergence. Main conclusions Anguilla bicolor has diverged between the Indian and Pacific oceans, which is consistent with the classical subspecies designation, but is apparently genetically homogeneous in the Indian Ocean. The analysis of gene‐flow and demographic history indicated that the two mitochondrial sublineages observed in the Indian Ocean probably represent the haplotype groups of relict ancestral populations. A comparison with a sympatric congener suggested that absolute physical barriers to gene flow may not be necessary for population divergence in eels.     

Population structure in two species of the reef goby<Emphasis Type="Italic"> Gnatholepis</Emphasis> (Teleostei: Perciformes) among four South Pacific island groups

Individuals of two species in the reef goby genus Gnatholepis ( G. anjerensis and G. scapulostigma) were sampled from across the South Pacific, including the Society Islands, the Tuamotu Archipelago, the Cook Islands, and Fiji. The two species examined differ in habitat preference, with one (G. anjerensis) preferring shallow, lagoon habitats, and the other (G. scapulostigma) usually occupying habitats outside the lagoons. Partial sequence of the mitochondrial ND2 gene (451–483 base pairs) was determined for 267 individuals and analyzed for demographic structure, population structuring, and correlation of population structure with geographic distance between populations. Both species exhibit demography characteristic of population expansion in the Pleistocene, approximately 88,000 years ago for G. anjerensis and 237,000 years ago for G. scapulostigma. Comparisons of _st indicate more structuring among populations of G. anjerensis than G. scapulostigma, although only G. scapulostigma shows a significant correlation between geographic distance and population divergence. It is postulated that the population expansions in Gnatholepis species are related to Pleistocene fluctuations in sea level, and that the ecology of G. anjerensis populations may contribute to their greater population structuring.Communicated by P.F. Sale     

Conclusive evidence for panmixia in the American eel

Eels are unique species in the biological world. The two North Atlantic eel species, the American eel (Anguilla rostrata) and the European eel (A. anguilla), occupy a broad range of habitats from the Caribbean to Greenland in the western Atlantic and from Morocco to Iceland in the eastern Atlantic, respectively. North Atlantic eels have a catadromous life cycle, spawning only in the Sargasso Sea and spending the majority of their lives in continental (fresh, brackish and coastal) waters. Despite such a wide distribution range, North Atlantic eels have been regarded as a textbook example of panmictic species. In contrast with the large amount of population genetic studies testing the panmixia hypothesis in the European eel, a relatively modest effort has been given to study the population structure of the American eel. In this issue of Molecular Ecology, Côté et al. ( 2013 ) present the most comprehensive American eel data set to date, which includes samples of different life stages obtained throughout all its distribution range in North America. Results show a total lack of genetic differentiation among samples and provide decisive evidence for panmixia in the American eel.     

Analysis of vertebral counts of the tropical anguillids, <Emphasis Type="Italic">Anguilla megastoma,A. obscura</Emphasis>, and <Emphasis Type="Italic">A. reinhardtii</Emphasis>, in the western South Pacific in relation to their possible population structure and phylogeny

The population structures of three tropical eel species, Anguilla megastoma, A. obscura, and A. reinhardtii, collected from several localities of each species range in the western South Pacific Ocean were evaluated using statistical analyses of total number of vertebrae (TV) data, which also included previously published data. There was a significant difference in TV values between Samoa and French Polynesia specimens of A. megastoma, while no significant difference was observed in TV data of A. obscura, despite the two species having similar overlapping species distribution ranges. There also was no significant difference found in the TV data of A. reinhardtii. These results suggest that A. megastoma may be separated into eastern and western populations in the western South Pacific, but there was no statistical evidence using the TV data that A. obscura and A. reinhardtii have population structure in the western South Pacific. These possible types of population structures are discussed in relation to the phylogeography and life histories of other tropical anguillid eels.     

Population Structure and Genetic Variability of Six Bar Wrasse (<Emphasis Type="Italic">Thallasoma hardwicki</Emphasis>) in Northern South China Sea Revealed by Mitochondrial Control Region Sequences

The genetic relationships among northern South China Sea populations of the six bar wrasse (Thallasoma hardwicki) were investigated. Fish collected from the Solomon Islands were used for geographic comparison. In 1998 and 1999, a total of 100 fish were sampled from 6 localities of the northern South China Sea and 3 localities of the Solomon Islands. Genetic variations in DNA sequences were examined from the first hypervariable region (HVR-1) of the mitochondrial control region, as amplified by polymerase chain reaction. High levels of haplotypic diversity (h = 0.944 ± 0.0016, = 0.0224 ± 0.01171) in the HVR-1 region of the mitochondrial control region of T. hardwicki were detected. This yielded 94 haplotypes that exhibited a minimum spanning tree with a starburst structure, suggestive of a very recent origin for most haplotypes. Neutrality tests indicated that the pattern of genetic variability in T. hardwicki is consistent either with genetic hitchhiking by an advantageous mutation or with population expansion. Partitioning populations into coherent geographic groups divided the northern South China Sea samples (_CT = 0.0313, P < 0.001) into 3 major groups: a north-central group composed of northwestern Taiwan and northern Vietnam; a southwestern group containing southern Vietnam; and a southern group including the central Philippines. These results are in concordance with mesoscale boundaries proposed by allozyme markers, thus highlighting the importance of identifying transboundary units for the conservation and management of fisheries in the South China Sea.     

Are Lithuanian eels fat enough to reach the spawning grounds?

Stocks of the European eel Anguilla anguilla have been in a steep decline since the 1980s. Stocking of water bodies with juvenile eels captured in the wild to establish or enhance local populations has been a common practise in Europe for many decades. However, the degree of contribution by stocked eels to natural spawning capacity is poorly known and extensively debated. There have been suggestions that eels derived from stocking are less likely to contribute to the spawning stock due to a lack of navigational capability and lower fitness related to insufficiency of energetic resources. Results of the current study indicated that eels translocated long distances from the point of capture and released into inland waters in Lithuania are successfully undergoing the silvering process. A proportion of 23.7% (N = 27) among all migrating eels were described to be at the yellow (SI, SFII or SFIII) eel stage and downstream movements of these eels should be attributed to local movements, rather than spawning migration; 76.3% were assigned to the silver eel stage. This study suggests that 36.8% (N = 32) of downstream migrating silver eels of stocked origin had accumulated sufficient energetic resources for spawning migration and gonadal development and should be able to traverse the 7900-km distance to the presumptive spawning grounds in the Sargasso Sea. The rest of migrating silver eels (63.2%, N = 55) had insufficient energetic resources; the average potential swimming range of these eels was estimated to be 6135 ± 683 km.     

Hierarchical genetic structure in fragmented populations of the Little Pocket Mouse (Perognathus longimembris) in Southern California

The geographic genetic structure, based onsequence variation of an 810 base pair fragmentof the mitochondrial cytochrome b gene,is described for populations of five subspeciesof the Little Pocket Mouse, Perognathuslongimembris, from Southern California. Oneof these, P. l. pacificus (Pacific PocketMouse), is listed as Endangered by the U.S.Federal Government. Sixty-two uniquehaplotypes were recovered from 99 individualssampled. Phylogenetic analyses of thesevariants do not identify regionallyreciprocally monophyletic lineages concordantwith the current subspecies designations, butmost haplotypes group by subspecies in networksgenerated by either statistical parsimony ormolecular variance parsimony. Moreover, asubstantial proportion of the total pool ofhaplotype variation is attributed to thesesubspecies, or to local populations withingeographic segments of each, indicating theirrelative evolutionary independence. The pooledextant populations of the endangered PacificPocket Mouse exhibit the same levels ofnucleotide and haplotype diversity as other,presumptively less-impacted populations ofadjacent subspecies, although the sample fromDana Point, Orange County, has markedly lowhaplotype diversity in comparison to allothers. These populations also show a geneticsignature of population expansion rather thanone of decline. Both pieces of evidence are atodds with current empirical populationestimates, which reinforces the fact thatpresent-day patterns of genetic diversity arethe product of coalescent history and will notnecessarily reflect recent anthropogenic, orother, perturbations. Comparison of haplotypevariation within and among extant populationsof the Pacific Pocket Mouse with those obtainedfrom museum samples collected more than 70years ago suggests that the pattern ofpopulation differentiation and diversity was inplace before the post-World War II exponentialurbanization of Southern California.     

A study on population genetic structure of Oryza meyeriana (Zoll. et Mor. ex Steud.) Baill. from Yunnan and its in situ conservation significance

In order to determine genetic diversity ofOryza meyeriana (Zoll. et Mor. ex Steud.) Baill., 12 enzyme systems encoded by 17 loci were electrophoretically analyzed in 164 individuals of seven populations from Simao Prefecture, Yunnan Province, China. In comparison with those seed plants with the same life history and breeding systems, as well as the other species in the genusOryza, the species shows rather low levels of genetic diversity (A = 1.1,P = 8.0 %, Ho = 0.004 and He = 0.015) within populations and high genetic differentiation among populations. F_st was up to 0. 649, suggesting that 64. 9% of total genetic variability exists among populations. Considering high genetic differentiation among populations from a limited geographic region, most of the populations of the species are worth being protected, and therefore, great natural protection regions should theoretically be established in which a great deal of populations should be involved for developingin situ conservation management. Meanwhile, some priory localities forin situ conservation ofO. meyerzana in Yunnan Province, were proposed. Project supported by the Grant of the President of the Chinese Academy of Sciences.     

Dams and canyons disrupt gene flow among populations of a threatened riparian plant

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Population Genetic Structure of the Ark Shell <Emphasis Type="Italic">Scapharca broughtonii</Emphasis> Schrenck from Korea,China, and Russia Based on <Emphasis Type="Italic">COI</Emphasis> Gene Sequences

Haplotype distribution, gene flow, and population genetic structure of the ark shell (Scapharca broughtonii) were studied using a partial sequence of a mitochondrial COI gene. The sequence analysis of 100 specimens obtained from a total of seven localities-five in Korea, one in China, and one in Russia- revealed 29 haplotypes, ranging in sequence divergence from 0.1% to 2.1%. Among these, the most frequent haplotype, SB16, was extensively distributed over study areas, especially in all Korean localities. This extensive distribution consequently resulted in the near absence of statistically significant genetic distance. Also, a high rate of gene flow was characteristic among localities in Korea. A test of genetic population structure showed that the ark shell in Korea formed a large genetic group. Moreover, an AMOVA test to determine the allocation of the genetic variance showed that most of the variance was distributed between localities, instead of within localities. However, a significant population differentiation was found between geographic populations [i.e., Jinhae (locality 6) in Korea and Sangdong (locality 5) in China and Vladivostok (locality 7) in Russia] based on geographic distance and population structure. These distinct groups may be associated with geographic characteristics and barriers. The results suggest that most of the ark shell populations in Korea caused considerable distribution to form a genetically homogeneous and intermixing structure, whereas some of the Korean and Chinese and Russian populations had a significantly different genetic structure.     

Seamounts, New Moon and eel Spawning: The Search for the Spawning Site of the Japanese eel

After analyzing all the collection data for larvae of the Japanese eel, Anguilla japonica, in the western North Pacific, we found that the spawning site of this species appears to be near three seamounts in the West Mariana Ridge, 2000–3000km away from their freshwater habitats. These seamounts are located in the westward flow of the North Equatorial Current and are hypothesized to provide cues for migrating silver eels and to serve as possible aggregation sites for spawning. Back-calculated birth dates based on otolith microstructure of leptocephali indicate that the Japanese eel does not spawn continuously during the long spawning season from April to November, but is synchronized to spawn periodically once a month during new moon. This lunar periodicity of spawning and the seamount spawning hypothesis are new developments in the millennium-old mystery of eel spawning that has fascinated naturalists since the time of Aristotle.