Vertical Distribution of Denitrification Potential,Denitrifying Bacteria,and Benzoate Utilization in Intertidal Microbial Mat Communities

Aspects of denitrification and benzoate degradation were studied in two estuarine microbial mat communities on the California coast by measuring the depth distributions of potential denitrification rates, genetic potential for denitrification, nitrate concentration, benzoate mineralization rates, total bacterial abundance, and abundance of a denitrifying strain (TBD-8b) isolated from one of the sites. Potential denitrification was detected in microbial mat cores from both Elkhorn Slough and Tomales Bay. Maximum denitrification rates were more than two orders of magnitude higher at Elkhorn Slough (3.14 mmol N m⁻² d⁻¹) than at Tomales Bay (0.02 mmol N m⁻² d⁻¹), and at both sites, the maximum rates occurred in the 0–2 mm depth interval. Ambient pore [NO₃+NO₂] was substantially higher at Elkhorn Slough than at Tomales Bay. Incorporation and mineralization of benzoate was maximal near the mat surface at Elkhorn Slough. The areal rate of benzoate utilization was 1045 nmol C m⁻² d⁻¹, which represented utilization of 70% of the added substrate in 24 h. Total bacterial and TBD-8b abundances were greatest near the surface at both Tomales Bay and Elkhorn Slough, and TBD-8b represented less than 0.2% of the total. Genetic potential for denitrification, quantified by hybridization with a nitrite reductase gene fragment, was present below the mat surface at average levels representing presence of the gene in approximately 10% of the total cells.     

Biological tags for stock separation in Pacific herring Clupea harengus pallasi in California.

A survey of the parasites of Pacific herring (Clupea harengus pallasi) off northern California identified 1 species of Acanthocephala, 1 species of Cestoda, 2 species of Copepoda, 1 species and 1 family of Digenea, 3 species of Nematoda, and 3 species of Protozoa. From this survey, Lacistorhynchus dollfusi (Cestoda), Parahemiurus merus (Digenea), and Anisakis simplex, Contracaecum sp., Hysterothylacium sp. (Nematoda) were selected as potential tags. Herring were collected in Tomales, San Francisco, and Monterey bays for the following 9 yr and examined for these select parasites. The results suggest that these parasites can be used to distinguish the spawning stocks of San Francisco and Tomales bays. The distribution of the definitive hosts of the respective parasites suggests that the Tomales Bay fish are offshore during the nonbreeding season and the San Francisco Bay fish onshore. The similarity in parasitism between San Francisco Bay and the nonspawning population in Monterey Bay suggests that these 2 populations represent a single stock.     

Genetic diversity in native and introduced populations of the amethyst gem clam Gemma gemma (Totten, 1834) from the U.S. east and west coasts

Reduced genetic diversity due to founder effects often is expected for invasive populations. The present study examined two nuclear gene regions and one mitochondrial gene to evaluate the origins and genetic diversity of Gemma gemma, a ‘stow-away’ that was introduced to California more than 100 years ago with the importation of the Eastern oyster, Crassostrea virginica, from the United States’ Atlantic coast. A previous investigation involving mitochondrial DNA cytochrome-c-oxidase subunit I sequences reported no significant difference in haplotype diversity between the native and introduced populations; however, estimates of allelic (or haplotypic) variability are insensitive to losses of rare alleles that may accompany founder events and population bottlenecks. Estimates of allele richness and the distribution of rare alleles provide more sensitive indicators of such events. The present investigation of introduced and potential source populations identified lower allele richness and number of singleton alleles in California samples. Atlantic coast Gemma exhibit a sharp phylogeographic transition between northeastern (New York through New England) and mid-Atlantic (southern New Jersey through Virginia) subpopulations, which appear latitudinally inverted for the California Gemma populations. These genetic results, and information from the transportation history of the Eastern oyster, help to clarify processes involved in the introduction of this invasive species.     

Geographic structure, genetic diversity and source tracking of Spartina alterniflora

Aim To examine the distribution and structure of genetic variation among native Spartina alterniflora and to characterize the evolutionary mechanisms underlying the success of non‐native S. alterniflora. Location Intertidal marshes along the Atlantic, Gulf and Pacific coasts of North America. Methods amova , parsimony analysis, haplotype networks of chloroplast DNA (cpDNA) sequences, neighbour‐joining analysis, Bayesian analysis of population structure, and individual assignment testing were used. Results Low levels of gene flow and geographic patterns of genetic variation were found among native S. alterniflora from the Atlantic and Gulf coasts of North America. The distribution of cpDNA haplotypes indicates that Atlantic coast S. alterniflora are subdivided into ‘northern’ and ‘southern’ groups. Variation observed at microsatellite loci further suggests that mid‐Atlantic S. alterniflora are differentiated from S. alterniflora found in southern Atlantic and New England coastal marshes. Comparisons between native populations on the Atlantic and Gulf coasts and non‐native Pacific coast populations substantiate prior studies demonstrating reciprocal interspecific hybridization in San Francisco Bay. Our results corroborate historical evidence that S. alterniflora was introduced into Willapa Bay from multiple source populations. However, we found that some Willapa Bay S. alterniflora are genetically divergent from putative sources, probably as a result of admixture following secondary contact among previously allopatric native populations. We further recovered evidence in support of models suggesting that S. alterniflora has secondarily spread within Washington State, from Willapa Bay to Grays Harbor. Main conclusions Underlying genetic structure has often been cited as a factor contributing to ecological variation of native S. alterniflora. Patterns of genetic structure within native S. alterniflora may be the result of environmental differences among biogeographical provinces, of migration barriers, or of responses to historical conditions. Interactions among these factors, rather than one single factor, may best explain the distribution of genetic variation among native S. alterniflora. Comprehensive genetic comparisons of native and introduced populations can illustrate how biological invasions may result from dramatically different underlying factors – some of which might otherwise go unrecognized. Demonstrating that invasions can result from several independent or interacting mechanisms is important for improving risk assessment and future forecasting. Further research on S. alterniflora not only may clarify what forces structure native populations, but also may improve the management of non‐native populations by enabling post‐introduction genetic changes and the rapid evolution of life‐history traits to be more successfully exploited.     

Stable carbon and nitrogen isotopes in multiple tissues of wild and captive harbor seals (Phoca vitulina) off the California coast

Stable carbon and nitrogen isotope ratios (δ¹³C and δ¹⁵N) of serum, red blood cells (RBC), muscle, and blubber were measured in captive and wild northeast Pacific harbor seals (Phoca vitulina richardii) at three coastal California sites (San Francisco Bay, Tomales Bay, and Channel Islands). Trophic discrimination factors (Δ_{Tissue‐Diet}) were calculated for captive seals and then applied in wild counterparts in each habitat to estimate trophic position and feeding behavior. Trophic discrimination factors for δ¹⁵N of serum (+3.8‰), lipid‐extracted muscle (+1.6‰), and lipid‐blubber (+6.5‰) are proposed to determine trophic position. An offset between RBC and serum of +0.3‰ for δ¹³C and ?0.6‰ for δ¹⁵N was observed, which is consistent with previous research. Specifically, weaner seals (<1 yr) had large offsets, suggesting strong trophic position shifts during this life stage. Isotopic values indicated an average trophic position of 3.6 at both San Francisco Bay and Tomales Bay and 4.2 at Channel Islands. Isotopic means were strongly dependent on age class and also suggested that mean diet composition varies considerably between all locations. Together, these data indicate that isotopic composition of blood fractions can be an effective approach to estimate trophic position and dietary behavior in wild pinnipeds.     

Survival probabilities and movements of harbor seals in central California

Harbor seal numbers and population trajectories differ by location in central California. Within San Francisco Bay (SFB) counts have been relatively stable since the 1972 Marine Mammal Protection Act, but in coastal areas like Tomales Bay (TB), counts increased before stabilizing in the 1990s. Emigration, poor survival, and environmental effects have been hypothesized as contributors to differences between trajectories; however, basic demographic data were not available to evaluate these hypotheses. We monitored 32 radio‐tagged adult females (SFB n = 17, TB n = 15) for 20 mo (2011–2013), and estimated survival, resight, and movement probabilities using mark‐resight analyses and multistate mark‐resight models. Annual survival probability for both sites was 0.90 (95% CI = 0.18–0.99). Six seals were observed moving between locations resulting in an estimated probability of 0.042 (95% CI = 0.023–0.076) per month equal movement between sites. Resight probability was less in SFB relative to TB, likely due to differential haul‐out access, area surveyed, visibility, and resight effort. Because of wide confidence intervals and low precision of these first estimates of adult female harbor seal survival in California, this demographic must be further examined to dismiss its contribution to differing population trajectories. Using aerial survey data, we estimated 950 harbor seals in SFB (95% CI = 715–1,184) confirming numbers are still stable.     

Global distribution of cryptic native,introduced and hybrid lineages in the widespread estuarine amphipod Ampithoe valida

Biological invasions can pose a severe threat to coastal ecosystems, but are difficult to track due to inaccurate species identifications and cryptic diversity. Here, we clarified the cryptic diversity and introduction history of the marine amphipod Ampithoe valida by sequencing a mtDNA locus from 683 individuals and genotyping 10,295 single-nucleotide polymorphisms (SNPs) for 349 individuals from Japan, North America and Argentina. The species complex consists of three cryptic lineages: two native Pacific and one native Atlantic mitochondrial lineage. It is likely that the complex originated in the North Pacific and dispersed to the north Atlantic via a trans-arctic exchange approximately 3 MYA. Non-native A. valida in Argentina have both Atlantic mitochondrial and nuclear genotypes, strongly indicating an introduction from eastern North America. In two eastern Pacific estuaries, San Francisco Bay and Humboldt Bay, California, genetic data indicate human-mediated hybridization of Atlantic and Pacific sources, and possible adaptive introgression of mitochondrial loci, nuclear loci, or both. The San Francisco Bay hybrid population periodically undergoes population outbreaks and profoundly damages eelgrass Zostera marina thalli via direct consumption, and these ecological impacts have not been documented elsewhere. We speculate that novel combinations of Atlantic and Pacific lineages could play a role in A. valida’s unique ecology in San Francisco Bay. Our results reinforce the notion that we can over-estimate the number of non-native invasions when there is cryptic native structure. Moreover, inference of demographic and evolutionary history from mitochondrial loci may be misleading without simultaneous survey of the nuclear genome.

     

Genetic variability and interpopulational differentiation of Artemia strains from South America

Seven Artemia samples from three South American countries (Chile, Brazil, Peru) were studied by starch electrophoresis with the aim of comparing levels of genetic variation and genetic similarity to representative populations of A. franciscana (San Francisco Bay, California, USA) and A. persimilis (Buenos Aires, Argentina), which are species endemic to the New World. Based on the analysis of 22 loci, parameters measuring genetic variability were, for some populations, found to be among the highest reported for Artemia so far. The percentage of polymorphic loci varied from 31.8% (Piura, Peru; Buenos Aires) to 50% (Los Vilos and Salar de Atacama, Chile), while the observed heterozygosity varied from 0.025 (Piura) to 0.165 (Los Vilos, Chile). A dendrogram based on Nei's genetic distance (D) produced four major groups. The Argentinian form, A. persimilis; the San Francisco Bay strain together with samples from Brazil (Macau and Rio Grande do Norte) and Chile (Pichilemu and Salar de Atacama); two coastal populations from Chile (Los Vilos and Iquique) and the sample from Peru (Piura). These four groups have inter-group D values that are, in some cases, far above those normally associated with conspecific populations.     

全球四大湾区生态环境综合评价研究

全球四大湾区既是经济发达区,也是生态环境脆弱区,对全球可持续发展至关重要。粤港澳大湾区的生态环境问题正在限制其可持续发展,有碍于全面建成国际一流湾区目标的实现。然而,过去的研究对生态环境方面关注较少,缺少湾区生态环境综合评价体系的构建。通过综合国内外统计和遥感多源数据,建立四大湾区生态环境评价数据库;围绕生态质量,环境质量和资源利用效率建立指标体系,构建湾区生态环境综合评价指数。结果表明：2015年,生态环境综合评价,东京湾区 > 旧金山湾区 > 纽约湾区 > 粤港澳大湾区;生态质量,纽约湾区 > 旧金山湾区 > 粤港澳大湾区 > 东京湾区;环境质量,旧金山湾区 > 东京湾区 > 纽约湾区 > 粤港澳大湾区;资源利用效率,东京湾区 > 旧金山湾区 > 纽约湾区 > 粤港澳大湾区。2005-2015年,粤港澳大湾区环境质量增速缓慢,在生态质量和资源利用效率增幅排名首位。旧金山湾区和纽约湾区优势在生态和环境质量,短板在资源利用效率;东京湾区在资源利用效率方面优势明显,短板在生态质量;综合来看,粤港澳大湾区与其他湾区都存在差距。研究建议粤港澳大湾区从生态空间、生态环境治理和资源利用方面,吸取发达国家湾区的经验。     

Extent and degree of hybridization between exotic (Spartina alterniflora) and native (S. foliosa) cordgrass (Poaceae) in California, USA determined by random amplified polymorphic DNA (RAPDs)

Spartina alterniflora, smooth cordgrass, native to the eastern USA, was introduced into south San Francisco Bay ≈ 25 years ago. It has spread by purposeful introduction of rooted plants and dispersal of seeds on the tides. Previous work suggested that S. alterniflora was competitively superior to the native California cordgrass, S. foliosa, and that the two species hybridized. The present study determined the spread of S. alterniflora and S. foliosa × alterniflora hybrids in California and examined the degree of hybridization. We used nuclear DNA markers diagnostic for each species to detect the parental species and nine categories of hybrids. The California coast outside San Francisco Bay contained only the native species. All hybrid categories exist in the Bay, implying that several generations of crossing have occurred and that hybridization is bidirectional. Hybrids were found principally near sites of deliberate introduction of the exotic species. Where S. alterniflora was deliberately planted, we found approximately equal numbers of S. alterniflora and hybrid individuals; S. foliosa was virtually absent. Marshes colonized by water-dispersed seed contained the full gamut of phenotypes with intermediate-type hybrids predominating. The proliferation of hybrids could result in local extinction of S. foliosa. What is more, S. alterniflora has the ability to greatly modify the estuary ecosystem to the detriment of other native species and human uses of the Bay. To the extent that they share these engineering abilities, the proliferation of cordgrass hybrids could grossly alter the character of the San Francisco Bay.     

The rapid evolution of self-fertility in Spartina hybrids (Spartina alterniflora × foliosa) invading San Francisco Bay, CA

Plant hybridization can lead to the evolution of invasiveness. We wished to determine whether hybrids between the largely self-sterile Atlantic Spartina alterniflora and California native S. foliosa had evolved self-fertility during their ca 30 year existence in San Francisco Bay, CA. In pollination experiments we found that neither of the parental species was self-fertile, nor were early generation hybrids. A large fraction of later generation hybrids were profusely self-fertile. Inbreeding depression was high in the parental species and early generation hybrids, but was much reduced in later generation hybrids—some even showed outbreeding depression. We found that populations of later generation hybrids and their seedling progeny were almost two-fold more homozygous than early generation hybrids, consistent with the evidence of increased selfing shown by our parentage analyses based upon 17 microsatellite markers. We posit that evolved self-fertility has contributed substantially to the rapid spread of hybrid Spartina in San Francisco Bay.     

Evolution of poecilogony from planktotrophy: cryptic speciation, phylogeography, and larval development in the gastropod genus Alderia

Poecilogony, a rare phenomenon in marine invertebrates, occurs when alternative larval morphs differing in dispersal potential or trophic mode are produced from a single genome. Because both poecilogony and cryptic species are prevalent among sea slugs in the suborder Sacoglossa (Gastropoda: Opisthobranchia), molecular data are needed to confirm cases of variable development and to place them in a phylogenetic context. The nominal species Alderia modesta produces long-lived, feeding larvae throughout the North Atlantic and Pacific, but in California can also produce short-lived larvae that metamorphose without feeding. We collected morphological, developmental, and molecular data for Alderia from 17 sites spanning the eastern and western Pacific and North Atlantic. Estuaries south of Bodega Harbor, California, contained a cryptic species (hereafter Alderia sp.) with variable development, sister to the strictly planktotrophic A. modesta. The smaller Alderia sp. seasonally toggled between planktotrophy and lecithotrophy, with some individuals differing in development but sharing mitochondrial DNA haplotypes. The sibling species overlapped in Tomales Bay, California, but showed no evidence of hybridization; laboratory mating trials suggest postzygotic isolation has arisen. Intra- and interspecific divergence times were estimated using a molecular clock calibrated with geminate sacoglossans. Speciation occurred about 4.1 million years ago during a major marine radiation in the eastern Pacific, when large inland embayments in California may have isolated ancestral populations. Atlantic and Pacific A. modesta diverged about 1.7 million years ago, suggesting trans-Arctic gene flow was interrupted by Pleistocene glaciation. Both Alderia species showed evidence of late Pleistocene population expansion, but the southern Alderia sp. likely experienced a more pronounced bottleneck. Reduced body size may have incurred selection against obligate planktotrophy in Alderia sp. by limiting fecundity in the face of high larval mortality rates in warm months. Alternatively, poecilogony may be an adaptive response to seasonal opening of estuaries, facilitating dispersal by long-lived larvae. An improved understanding of the forces controlling seasonal shifts in development in Alderia sp. may yield insight into the evolutionary forces promoting transitions to nonfeeding larvae.     

Cryptic diversity of Melanochlamys sea slugs (Gastropoda,Aglajidae) in the North Pacific

North Pacific specimens of Melanochlamys sea slugs were examined morphologically (including the male reproductive morphology, shell and external coloration) and were sequenced for three genes (mitochondrial COI and 16S and nuclear H3). Phylogenetic and species delimitation analyses were used to determine the evolutionary relationships and species diversity among the specimens examined. Both molecular and morphological data revealed an unexpected high level of cryptic diversity. At least four distinct species occur on the Northwestern Pacific. Melanochlamys ezoensis occurs in Russia and temperate and cold areas in Japan. Three additional undescribed species occur in Japan and/or South Korea. One of the undescribed species occurs both in South Korea and in Japan, but only in Tokyo Bay, suggesting that it could be non‐native in Japan. Two distinct species occur on the Northeastern Pacific coast; Melanochlamys diomedea is widespread from Southern California to Alaska, whereas M. ezoensis was found only in San Francisco Bay, suggesting a human‐mediated introduction. This is further supported by the absence of records of M. ezoensis in San Francisco prior to 2001. The species diversity of Melanochlamys in the Northwestern Pacific is much greater than in the Northeastern Pacific; it is hypothesized that differences in geographic and ocean current system complexity might account for different responses to glacial extinction and postglacial expansion.     

PATTERNS OF REPRODUCTION,GENETIC DIVERSITY,AND GENETIC DIFFERENTIATION IN CALIFORNIA POPULATIONS OF THE GENICULATE CORALLINE ALGA LITHOTHRIX ASPERGILLUM (RHODOPHYTA)1

The reproductive composition and genetic diversity of populations of the red seaweed Lithothrix aspergillum Gray (O. Corallinales) were studied at three southern California sites (Shaw's Cove and Treasure Island, Laguna Beach; Indian Rock, Santa Catalina Island) and at a fourth site (Bodega Bay) located in northern California. Sexually reproducing populations were confined to southern California. Diploid individuals were numerically dominant over haploid (gametophytic) individuals at all sites. Intertidal and subtidal subpopulations from Shaw's Cove differed in their reproductive profiles. Most intertidal specimens found on emersed surfaces were densely branched, turf-forming, and bore tetrasporangial (68.6%), carposporangial (11.4%), or spermatangial (5.7%) conceptacles, reflecting a sexual life history; none produced asexual bispores. In contrast, 74.3% of the larger, loosely branched subtidal specimens bore bisporangial conceptacles indicative of asexual reproduction. Nearly 70% of the Indian Rock thalli showed no evidence of conceptacle formation. Only asexual, diploid bispore-producing thalli were obtained from the Bodega Bay site. Genetic diversity (mean number of alleles per locus, percent of polymorphic loci, and average expected heterozygosity) of diploid L. aspergillum populations varied with life-history characteristics and geographic location. A total of 30 alleles was inferred from zymograms of 16 loci examined by starch-gel electrophoresis; of these loci, 11 were polymorphic. The genetic diversity of sexual, diploid populations of L. aspergillum (alleles per locus [A/L] = 1.4-1.5; percent polymorphic loci [%P] = 37.5-50.0) was relatively high compared with other red seaweeds. Lowest diversity (A/L = 1.0; %P = 0.0) occurred in the exclusively asexual Bodega Bay population which consisted of genetic clones. All sexual L. aspergillum populations deviated significantly from Hardy-Wein-berg expectations due to lower than expected heterozygosity. Genetic differentiation (Wright's F_statistic [F_ST]; Nei's Genetic Distance [D]) among sexually reproducing southern California populations was low (F_ST= 0.030) on a local scale (ca. 5 km), suggesting high levels of gene flow, but high genetic differention (F_ST= 0.390 and 0.406) occurred among southern California populations separated by ca. 70 km. Very high genetic differentiation (F_ST= 0.583–0.683) was obtained between northern and southern California populations separated by 700–760 km. Our genetic and reproductive data suggest that the L. aspergillum population from Bodega Bay is sustained by perennation, vegetative propagation, or asexual reproduction by bispores and may represent an isolated remnant or a population established by a founder event.     

Habitat Differences in Marine Invasions of Central California

We carried out a two-part investigation that revealed habitat differences in marine invertebrate invasions. First, we compared invasion levels of hard vs soft substrata in Elkhorn Slough, an estuary in Central California, by comparing abundance and richness of native vs exotic species in quantitative samples from each habitat type. Our results revealed that the hard substrata were much more heavily invaded than the soft substrata. Nearly all the hard substrata in Elkhorn Slough, as in most estuaries along the Pacific coast of North America, are artificial (jetties, rip-rap, docks). Some exotic species may by chance be better adapted to this novel habitat type than are natives. Two major vectors responsible for marine introductions, oyster culturing and ship-hull fouling, are also more likely to transport species associated with hard vs soft substrata. Secondly, we compared estuarine and open coast invasion rates. We examined species richness in Elkhorn Slough and adjacent rocky intertidal habitats along the Central California coast. The absolute number of exotic species in the estuary was an order of magnitude higher than along the open coast (58 vs 8 species), as was the percentage of the invertebrate fauna that was exotic (11% vs 1%). Estuaries on this coast are geologically young, heavily altered by humans, and subject to numerous transport vectors bringing invasive propagules: all these factors may explain why they are strikingly more invaded than the open coast. The finding that the more species rich habitat – the open coast – is less invaded is in contrast to many terrestrial examples, where native and exotic species richness appear to be positively correlated at a broad geographic scale.     

A new species of Mysidobdella (Hirudinida: Piscicolidae) from mysids along the California coast

Mysidobdella californiensis n. sp. is described from the mysid Holmesimysis sculpta from Bodega Bay on the central California coast and from Holmesimysis costata var. from San Pedro on the southern California coast. The internal anatomy of M. californiensis is similar to that of the only other species in the genus, Mysidobdella borealis from the north Atlantic Ocean, except that M. californiensis lacks the medial, unpaired seminal receptacle present in M. borealis. Externally, M. californiensis is slightly larger and more robust than M. borealis, with a much larger caudal sucker. The most striking difference between the species is the unusually large, trumpet-shaped, fluted oral sucker in M. californiensis. At Bodega Bay, the prevalence of M. californiensis on its host was 17% with an average intensity of 1.46 (range 1-3) leeches per host.     

Tidal movements of female leopard sharks (<Emphasis Type="Italic">Triakis semifasciata</Emphasis>) in Elkhorn Slough,California

The leopard shark (Triakis semifasciata) is one of the most common species of elasmobranch in California, and uses the shallow bays and estuaries of California extensively throughout its life history. To examine the role that tides and time of day play on the distribution and movements of leopard sharks in an estuarine environment, a total of 22 female leopard sharks (78–140 cm TL) were tagged with acoustic transmitters in Elkhorn Slough, California, USA. Eight sharks were manually tracked for 20–71.5 h, and 13 sharks were monitored for 4–280 days using an array of acoustic receivers. Overall, the distribution and movements of sharks were strongly influenced by the tides and to a lesser extent by period of day, although general patterns of movement differed depending on what region of Elkhorn Slough the sharks were using. In the main channel of Elkhorn Slough, sharks generally moved with the tide, maximizing the area over which they could forage on a more dispersed prey field. Conversely, leopard sharks within the Elkhorn Slough National Estuarine Research Reserve regularly swam against strong currents to remain in proximity to the intertidal mudflats. This high degree of fidelity to a specific region was probably due to an abundance of important prey in the area. These results indicate that movements, and thus the foraging ecology, of leopard sharks show a high degree of plasticity and are influenced by tidal stage, tidal current, availability of suitable habitat, and availability and distribution of important prey items.     

An introduced population of Chorda asiatica (Chordaceae,Laminariales) in Puget Sound,Pacific coast of North America

Northeastern Pacific Ocean and northwestern Atlantic Ocean populations of Chorda species, which have not been examined in previous phylogenetic studies, were investigated. All specimens that were collected in Hood Canal, Puget Sound, WA, USA, Pacific coast of North America, showed identical ITS‐5.8S rDNA sequences, and they were included in the clade of Japanese Chorda asiatica. With morphological data added to the molecular data, they were identified as C. asiatica and were concluded to be non‐indigenous populations, most likely introduced with oyster spat together with Sargassum muticum. Specimens collected in New York, NY, USA, Atlantic coast of North America, were genetically closest to C. filum from Newfoundland and were identified as C. filum. The genetic divergence of the North Atlantic populations of C. filum was relatively small compared to that of Japanese C. asiatica considering their broader distributional ranges on both sides of the Atlantic.     

Food habits of harbor seals (Phoca vitulina richardii) as an indicator of invasive species in San Francisco Bay,California

The diet of harbor seals (Phoca vitulina richardii) in San Francisco Bay (SFB), California, was determined from July 2007 to July 2008 using prey hard parts recovered from 442 scats collected at five haul‐out sites. Twenty‐two species of fish and one species of crustacean were identified, but harbor seals primarily ate a nonnative invasive species, yellowfin goby (Acanthogobius flavimanus), which increased in dietary importance since the diet was last studied in 1991/1992. Additionally, another nonnative invasive fish species, chameleon goby (Tridentiger trigonocephalus), was found for the first time in the diet of harbor seals in SFB. Harbor seal diet was statistically different between years (1991/1992 and 2007/2008), between the pupping and nonpupping seasons, and between North SFB and South SFB haul‐out locations. The diet of harbor seals was significantly correlated with fish species caught in trawl surveys conducted by the California Department of Fish and Wildlife (CDFW) during the same time periods as this study (2007/2008). Harbor seals currently are influencing the health of the SFB ecosystem in a positive manner by consuming large quantities of nonnative invasive fish species.     

A century of landscape disturbance and urbanization of the San Francisco Bay region affects the present-day genetic diversity of the California Ridgway’s rail (<Emphasis Type="Italic">Rallus obsoletus obsoletus</Emphasis>)

Fragmentation and loss of natural habitat have important consequences for wild populations and can negatively affect long-term viability and resilience to environmental change. Salt marsh obligate species, such as those that occupy the San Francisco Bay Estuary in western North America, occupy already impaired habitats as result of human development and modifications and are highly susceptible to increased habitat loss and fragmentation due to global climate change. We examined the genetic variation of the California Ridgway’s rail (Rallus obsoletus obsoletus), a state and federally endangered species that occurs within the fragmented salt marsh of the San Francisco Bay Estuary. We genotyped 107 rails across 11 microsatellite loci and a single mitochondrial gene to estimate genetic diversity and population structure among seven salt marsh fragments and assessed demographic connectivity by inferring patterns of gene flow and migration rates. We found pronounced genetic structuring among four geographically separate genetic clusters across the San Francisco Bay. Gene flow analyses supported a stepping stone model of gene flow from south-to-north. However, contemporary gene flow among the regional embayments was low. Genetic diversity among occupied salt marshes and genetic clusters were not significantly different. We detected low effective population sizes and significantly high relatedness among individuals within salt marshes. Preserving genetic diversity and connectivity throughout the San Francisco Bay may require attention to salt marsh restoration in the Central Bay where habitat is both most limited and most fragmented. Incorporating periodic genetic sampling into the management regime may help evaluate population trends and guide long-term management priorities.