Dynamics and population genetics of Pinna rudis in the Tyrrhenian Sea: Exploring the potential link to the local extinction of Pinnanobilis.

Over the last few decades, advances in molecular techniques have led to the detection of strong geographic population structure and cryptic speciation in many benthic marine taxa, even those with long-lived pelagic larval stages. Polychaete annelids, in particular, generally show a high degree of population divergence, especially in mitochondrial genes. Rarely have molecular studies confirmed the presence of 'cosmopolitan' species. The amphinomid polychaete Hermodice carunculata was long considered the sole species within its genus, with a reported distribution throughout the Atlantic and adjacent basins. However, recent studies have indicated morphological differences, primarily in the number of branchial filaments, between the East and West Atlantic populations; these differences were invoked to re-instate Hermodice nigrolineata, formerly considered a junior synonym of H.carunculata. We utilized sequence data from two mitochondrial (cytochrome c oxidase subunit I, 16S rDNA) markers and one nuclear (internal transcribed spacer) marker to examine the genetic diversity of Hermodice throughout its distribution range in the Atlantic Ocean, including the Mediterranean Sea, the Caribbean Sea, the Gulf of Mexico and the Gulf of Guinea. Our analyses revealed generally low genetic divergences among collecting localities and between the East and West Atlantic, although phylogenetic trees based on mitochondrial data indicate the presence of a private lineage in the Mediterranean Sea. A re-evaluation of the number of branchial filaments confirmed differences between East and West Atlantic populations; however, the differences were not diagnostic and did not reflect the observed genetic population structure. Rather, we suspect that the number of branchial filaments is a function of oxygen saturation in the environment. Our results do not support the distinction between H.carunculata in the West Atlantic and H.nigrolineata in the East Atlantic. Instead, they re-affirm the older notion that H.carunculata is a cohesive species with a broad distribution across the Atlantic Ocean.

The aim of this study was to determine the influence of biogeography, oceanography and ecology on the population structure of different crustacean species with emphasis on their larval development. It is predicted that the duration of larval development influences the dispersal capability and therefore the level of genetic differentiation. In addition, the results should provide answers if there are cryptic species. The two atlanto-mediterranean crab species Xantho hydrophilus (Herbst, 1790) and Xantho poressa (Olivi, 1792) and the European prawn Palaemon elegans (Rathke, 1837) were included as marine species. Xantho has a shorter larval development with four zoeal stages than Palaemon with nine larval stages. Therefore, a higher gene flow within Palaemon was expected. We used also the amphidromous species Xiphocaris elongata (Guérin-Méneville, 1856) which occurs in freshwater systems of the Caribbean islands. The life cycle of amphidromous X. elongata is intermediate between freshwater and marine species and thus, high genetic differentiation was predicted. A comparative population genetics analyses was conducted to reveal differences in the population structure due to the distinct larval development and the amphidromous life-cycle. In the case of X. hydrophilus, results show a restricted gene flow between the populations of the Atlantic and the Mediterranean Sea. However, the taxonomic status of the Mediterranean subspecies X. h. granulicarpus is not valid as long as no single mutation step was detected to distinguish constantly between the two subspecies X. hydrophilus and X. h. granulicarpus. In addition, morphological transitional forms of X. hydrophilus are found within the Western Mediterranean Sea. X. poressa is suggested to reproduce panmictically because no differences are found between the populations of the Mediterranean Sea and the Atlantic Ocean and a mark recapture experiment showed that the species reaches high population densities. This species is well adapted to its habitat due to its variability in colouration and size which is the result of passive defence (camouflage). A pattern of allometric growth in the carapace shape was observed. Phylogenetic analyses revealed that X. sexdentatus is very closely related to X. hydrophilus. This could be either due to hybridization or introgression. Despite the fact that Palaemon elegans has nine larval stages, there is surprisingly high genetic differentiation. Normally such strong differences are only found between species and thus a cryptic species within the P. elegans complex is suggested. Three types of haplotype groups are found: Type I from the Atlantic and the Alboran Sea, Type II only within the Mediterranean Sea and Type III within the Mediterranean, Black, Caspian, Baltic and East Sea. Type III could be a relict of the Messinian crisis due to its high genetic differentiation, while Type II has recolonized the Mediterranean Sea after the crisis and ongoing separation mechanisms have established restricted gene flow between Type I and II. The barrier to gene flow between the Atlantic Type and the two Mediterranean Types is the Almería-Oran-Front. The Almería-Oran-Front is an important phylogeographic break, where restricted gene flow is possible. An isolation-by-distance pattern could be detected within the Atlantic Ocean. Furthermore, there is significant genetic differentiation between the Northern Atlantic and the North-East Atlantic due to the English Channel. These results provide evidence that dispersal play a minor role in determining the genetic structure of a species, compared to the biogeographic history and physical factors. This becomes even more obvious by comparison with the shrimp Xiphocaris elongata, for which a higher genetic differentiation due to the isolated freshwater systems and the amphidromous life cycle was expected. Although there is a high genetic differentiation, no geographic pattern emerges. The amphidromous life cycle enhance the dispersal capability and gene flow. It displays rather patterns of a marine species than of an exclusively freshwater species. The species is characterized by its variability in the rostrum length, but the results give no evidence for a genetic differentiation of the phenotypes. Thus, adaptive plasticity due to predators and in part allometric growth could be an explanation for the variability.

The loliginid squids Loligo pealei LeSueur and L. plei Blaineville (both recently proposed for reclassification as Doryteuthis) are commercially important, similar in appearance, and sympatric throughout much of the northwestern Atlantic Ocean, the Gulf of Mexico, and the Caribbean Sea. To investigate possible cryptic speciation and population structure, we examined samples (collected from 1995 to 1997) of both species for restriction fragment length polymorphisms (RFLPs) in PCR products of the mitochondrial gene cytochrome c oxidase (subunit I). RFLP haplotypes were further characterized by direct sequencing. In North American waters, cryptic speciation was rejected by the far greater nucleotide sequence divergence between species (~14%) versus within species (<1%). Each species displayed about a dozen RFLP haplotypes, but only three of their respective haplotypes were found among 90% of L. pealei specimens (n=356) and 97% of L. plei specimens (n=431). For L. pealei, a genetic break existed between the northern Gulf of Mexico and the Atlantic Ocean; among sample units within each population, gene flow was consistent with panmixia. The phylogeography of L. pealei is likely a consequence of the eastward currents of the Florida Straits, the elevated temperatures of those surface waters, and the restriction of this species to the continental shelf. For L. plei, a genetic break existed between longitudes 88°W and 89°W, with the northwestern Gulf of Mexico and the northeastern Gulf–Atlantic Ocean comprising separate populations; among sample units within each population, gene flow fit an isolation-by-distance model. If the genetic break found for L. plei represents resident populations separated by nearshore physical parameters (e.g. effects of the Mississippi River and the sediment boundary at longitude 88°W), the lack of structure within the Gulf for L. pealei might be due to its distribution farther from shore. However, the two populations of L. plei probably represent annual recolonization from the southwestern Gulf of Mexico and from the eastern Caribbean Sea, whereas the populations of L. pealei probably are permanent residents within their respective regions.

Crotalaria is a plant genus that is found all over the world, with over 700 species of herbs and shrubs. The species are potential alternative food and industrial crops due to their adaptability to different environments. Currently, information on the genetic diversity and population structure of these species is scanty. Genotyping-by-sequencing (GBS) is a cost-effective high-throughput technique in diversity evaluation of plant species that have not been fully sequenced. In the current study, de novo GBS was used to characterize 80 Crotalaria accessions from five geographical regions in Kenya. A total of 9820 single nucleotide polymorphism (SNP) markers were obtained after thinning and filtering, which were then used for the analysis of genetic diversity and population structure in Crotalaria. The proportion of SNPs with a minor allele frequency (maf) > = 0.05 was 45.08%, while the Guanine-Cytosine (GC) content was 0.45, from an average sequence depth of 455,909 reads per base. The transition vs transversion ratio was 1.81 and Heterozygosity (He) ranged between 0.01–0.07 in all the sites and 0.04 to 0.52 in the segregating sites. The mean Tajima’s D value for the population was -0.094, suggesting an excess of rare alleles. The fixation index (Fst) between the different populations based on the Wright Fst (1943) ranged from 0.0119 to 0.066 for the Eastern-Western and Nairobi-Western populations. Model based techniques of population structure analysis including structure, k-means and cross-entropy depicted eight clusters in the study accessions. Non-model based techniques especially DAPC depicted poor population stratification. Correspondence Analysis (CA), Principal coordinate analyses (PCoA) and phylogenetic analysis identified a moderate level of population stratification. Results from this study will help conservationists and breeders understand the genetic diversity of Crotalaria. The study also provides valuable information for genetic improvement of domesticated species.

AimUnderstanding cetacean species' distributions and population structure over space and time is necessary for effective conservation and management. Geographic differences in acoustic signals may provide a line of evidence for population‐level discrimination in some cetacean species. We use acoustic recordings collected over broad spatial and temporal scales to investigate whether global variability in echolocation click peak frequency could elucidate population structure in Blainville's beaked whale (Mesoplodon densirostris), a cryptic species well‐studied acoustically.LocationNorth Pacific, Western North Atlantic and Gulf of Mexico.Time period2004–2021.Major taxa studiedBlainville's beaked whale.MethodsPassive acoustic data were collected at 76 sites and 150 cumulative years of data were analysed to extract beaked whale echolocation clicks. Using an automated detector and subsequent weighted network clustering on spectral content and interclick interval of clicks, we determined the properties of a primary cluster of clicks with similar characteristics per site. These were compared within regions and across ocean basins and evaluated for suitability as population‐level indicators.ResultsSpectral averages obtained from primary clusters of echolocation clicks identified at each site were similar in overall shape but varied in peak frequency by up to 8 kHz. We identified a latitudinal cline, with higher peak frequencies occurring in lower latitudes.Main conclusionsIt may be possible to acoustically delineate populations of Blainville's beaked whales. The documented negative correlation between signal peak frequency and latitude could relate to body size. Body size has been shown to influence signal frequency, with lower frequencies produced by larger animals, which are subsequently more common in higher latitudes for some species, although data are lacking to adequately investigate this for beaked whales. Prey size and depth may shape frequency content of echolocation signals, and larger prey items may occur in higher latitudes, resulting in lower signal frequencies of their predators.

ABSTRACTThis study investigated a typical pine-oak mosaic mixed forest in the Qinling Mountains, China. In the sample plot, the population structure and spatial distribution of the stems were analyzed for the predominant species, to identify the mechanisms of species coexistence and successional trends of the forest. The population structures of all species were bimodally distributed, with young trees (DBH <1 cm) more abundant than older trees. The population structures of Quercus aliena var. acuteserrata was bimodal and rather continuous. However, Pinus tabuliformis and Pinus armandii were discontinuously bimodal, with distinct size deficiencies. Q. aliena var. acuteserrata trees were clumped throughout the plot, although those of P. tabuliformis and P. armandii were clumped at small scales. Notable negative spatial associations between Q. aliena var. acuteserrata and P. tabuliformis were found at almost scales. P. armandii and Q. aliena var. acuteserrata were negatively spatially associated at small scales but positively associated at large scales. Our findings suggest that interspecific competition gradually develops among the predominant tree species. The dynamics of the pine-oak mosaic mixed forest formed a mosaic distribution of uniformly mixed types, with the slow infiltration of Q. aliena var. acuteserrata populations that would eventually establish a pure stand.

Genetic diversity of Culicoides species within the Pulicaris complex (Diptera: Ceratopogonidae) in Turkey inferred from mitochondrial COI gene sequences

Phenetic structure of two Bactrocera tau cryptic species (Diptera: Tephritidae) infesting Momordica cochinchinensis (Cucurbitaceae) in Thailand and Laos

The forest ecosystems have been essential to the survival and existence of humans but are one of the most threatened ecosystems on the globe. For the sake of their diversity and continued existence, natural forests must be preserved. The population structure, diversity, and distribution of tree species offer fundamental data for the management and conservation of forests. To comprehend the pattern of species diversity and the status of regeneration in the core and buffer areas of Sawai Mansingh Sanctuary in Rajasthan, the current work aims to provide information on phytosociological attributes. Nested random quadrate sampling is used in the study; 20 quadrates of size 100m×100m were randomly laid in both the area (core and buffer area) for tree sampling, and within each such quadrate lie 4 quadrates of 10m×10m for saplings and 4 quadrates of 1m×1m were drawn in the above quadrates for seedlings. The study area harbors tropical dry deciduous thorny forest; 37 species of 32 genera and 22 families were recorded from the core area, and 24 species, 21 genera, and 15 families were recorded from the buffer area. In the core area, the highest density was contributed by Anogeissus pendula Edgew, whereas in the buffer area, the contribution of Prosopis juliflora (L.) Druce is highest. Basal areas covered by trees for the core area showed a total of 105.79 m² hectare⁻¹, while the total basal area of the buffer zone is 21.56 m² hectare⁻¹. In the case of the core region, the main contributor to the basal area is Butea monosperma (Lam.) Taubert because of its higher girth class than Anogeissus pendula Edgew, whereas in the buffer zone, Prosopis juliflora (L.) Druce contributed most to the total basal area. The core zone shows normal regeneration, with the highest percentage of tree species showing fair regeneration; the buffer zone shows discontinuous or irregular recruitment of individuals. The cumulative girth class basal area and the number of individual distribution patterns in the buffer area reveal that the density of woody species in some classes is high and low or absent altogether in other classes, reflecting the area's generally poor regeneration profile.

ABSTRACTClimatic variability significantly impacts global fisheries by altering oceanographic conditions, potentially affecting fishing yields and species composition, and studying climate change's effects is crucial for understanding marine ecosystems, predicting disruptions and informing sustainable management strategies. Hence, this study examined the impact of climatic variability on pelagic predators like tunas, marlins and swordfish, using fishery data from 2005, January to 2016, December, focusing on nine commercially significant species each from the Indian and South Atlantic oceans. The hypothesis of the study was composed of two parts, that is, different populations of same species in the Indian and South Atlantic Ocean may respond differently to climatic variability, and the impact of teleconnections on fisheries may vary across these two oceans. The first part of the current study involved evaluating the importance of climatic variability on species using generalised additive modelling, while the second part involved analysing the unique effects of species‐specific climatic variability using cross‐spectral and cross‐wavelet analysis. The current study revealed two significant findings: firstly, species in the Indian Ocean and South Atlantic Ocean had distinct response to climatic variability (first hypothesis), and secondly, the species in the Indian Ocean displayed a higher level of sensitivity to teleconnection impacts (second hypothesis). The study's findings can help fisheries communities to anticipate and adapt to changes in fish distribution and productivity, enhancing their practices and spatial management, thereby promoting sustainable global fisheries management.

Mass mortality events of benthic invertebrates in the temperate north-western (NW) Mediterranean Sea have been observed in recent seasons. A 16 month in situ study in the Ligurian Sea (NW Mediterranean Sea) demonstrated that the occurrence of Paramuricea clavata mortality episodes were concomitant to a condition of prolonged high sea surface temperatures, low chlorophyll concentrations and the presence of culturable Vibrio spp. in seawater. The occurrence of Vibrio spp. at the seasonal scale was correlated with temperature; with few vibrios retrieved on specific media when the temperature dropped below 18 degrees C and a sharp increase of vibrios abundance (up to 3.4 x 10(4) MPN l(-1)) when the temperature was greater than or equal to 22 degrees C. Phylogenetic and phenotypic analysis of Vibrio isolates associated with healthy and diseased P. clavata colonies collected during a mortality episode showed that these bacteria were significantly more abundant in diseased than in healthy corals and were related to the V. harveyi, V. splendidus and V. coralliilyticus groups, the latter only identified in diseased organisms. Inoculation of bacterial isolates from these groups onto healthy P. clavata in aquaria caused disease signs and death in a range of Vibrio concentrations, temperature values and trophic conditions consistent with those recorded in the field. It is concluded that Vibrio infections may act as an additional triggering mechanism of mass mortality events in the coastal Mediterranean Sea and that their occurrence is climate-linked. Predicted global warming leading to long-lasting hot summer periods together with stratification resulting in energetic constraints represent a major threat to the survival of benthic invertebrates in the temperate NW Mediterranean Sea due to potential disease outbreak associated with Vibrio pathogens.

Comparative works on sampling techniques allow selecting the best methods to study each target fish community. We analysed the structure of a coastal fish community in Galicia (north-western Spain) by comparing the following three techniques: diver-based underwater visual census (UVC), remotely operated vehicle (ROV) and remote underwater video (RUV). All techniques detected abundant and frequent taxa, but divers obtained more precise and complete inventories (80% of identified taxa) than did ROV (60%) and RUV (47%), were faster (only 1.4 days to achieve the estimated taxa list) than were ROV (2.0 days) and RUV (475.7 days), and were more reliable in estimating the abundances of highly mobile, less abundant, less frequent, cryptic and smaller fish. Conversely, RUV obtained the poorest estimates of abundances, and even though it obtained more replicates (136), there were more zeros (98%) than with divers (16 replicates, 64% zeros) and ROV (11 replicates, 75% zeros). Furthermore, the economic cost of the video system was triple the cost of the diving gear; consequently, we recommend using divers to study the coastal fish communities in the shallow waters of the North Atlantic Ocean. However, further research is necessary to explore the full capabilities of video techniques in long-term studies, in greater depths and in adverse weather conditions.

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 362:245-259 (2008) - DOI: https://doi.org/10.3354/meps07410 Effects of fishing on population structure and life history of roman Chrysoblephus laticeps (Sparidae) Albrecht Götz1,2,*, Sven E. Kerwath1, Colin G. Attwood3, Warwick H. H. Sauer1 1Department of Ichthyology and Fisheries Science, Rhodes University, 6140 Grahamstown, South Africa 2Elwandle Node, South African Environmental Observation Network (SAEON), 6140 Grahamstown, South Africa 3Marine Research Institute, Zoology Department, University of Cape Town, Private Bag X3, 7701 Rondebosch, South Africa *Email: albrecht@saeon.ac.za ABSTRACT: The effects of fishing on the population structure and life history of roman Chrysoblephus laticeps, a protogynous hermaphroditic seabream from South Africa, were investigated by comparing fish from protected and exploited areas. Experimental (controlled) fishing and underwater visual census were used to sample roman and to measure population parameters inside and outside the Goukamma Marine Protected Area. Sites chosen for comparisons were adjacent and physically similar to reduce environmental influences on the comparison. Both methods revealed that roman had a higher density and mean size inside the protected area than outside. Age-at-maturity and age-at-sex-change were lower in the exploited area. The shift in age-at-sex-change maintained a constant sex ratio between the exploited and unexploited areas. The condition factor of roman from the protected area was lower than that of roman from the exploited area. KEY WORDS: Fishing effects · Life history · Population structure · Chrysoblephus laticeps · Sparidae · Marine protected area · Sex change Full text in pdf format PreviousNextCite this article as: Götz A, Kerwath SE, Attwood CG, Sauer WHH (2008) Effects of fishing on population structure and life history of roman Chrysoblephus laticeps (Sparidae). Mar Ecol Prog Ser 362:245-259. https://doi.org/10.3354/meps07410 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 362. Online publication date: June 30, 2008 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2008 Inter-Research.

The morphological identification of cryptic rodent species has historically been problematic. At best, many cryptic species have been identified by chromosomal differences. However, to study the life histories of such rodent species, there is a need for a molecular technique for cryptic species identification that does not involve destructive sampling. In this manuscript we examine mitochondrial DNA (mtDNA) cytochrome-b genetic variation in 2 cryptic murid rodent species, the red veld rat (Aethomys chrysophilus) and the Tete veld rat (A. ineptus) from southern Africa. Phylogenetic and phylogeographic analyses of these sequences showed reciprocal monophyly between populations of the 2 species in southern Africa, but no support for monophyly of A. chrysophilus from southern and eastern Africa. This suggests that the analysis of mtDNA can be used to distinguish these 2 sister species in southern Africa. However, these results need to be investigated further by DNA analyses of type specimens, topotypical material, or both from adjacent localities.

The endemic bivalve Pinna nobilis is the largest bivalve in the Mediterranean Sea and one of the largest worldwide, able to reach 1 m or more in size. During recent decades, P. nobilis populations have suffered substantial declines due to several causes of anthropogenic origin. The species situation is currently critical throughout the Mediterranean Sea due to a mass mortality event (MME) that started in late 2016. Recent findings indicate that a picornavirus had compromised the fan mussel immune system, enabling the protozoan Haplosporidium pinnae to infect immunosuppressed individuals and cause most die-offs. As a result, this bivalve has been included in the Spanish National Catalog of Threatened Species and the IUCN Red List since 2020. The present study aims to improve the knowledge of the status of P. nobilis populations between 2010 and 2023 in the Tabarca Marine Reserve, the first Spanish marine reserve. Before the MME, density reached 2.8 ind. 100 m -2 in this marine reserve. P. nobilis density varied significantly with the bottom type-depth interaction, whereas size was associated with depth and island zone. Following the MME, mortality of pen shells reached 100%. Thereafter, an increase in Pinna rudis abundance was detected, occupying the spaces left by P. nobilis after its disappearance. In addition, a putative hybrid P. nobilis × P. rudis was detected. These results contribute to the knowledge of the species population status in this marine protected area, and provide useful information, in case of recovery in the future, to facilitate the implementation of management policies.