Mitochondrial Control Region Sequences Research Articles

Brown trout in Japan − introduction history, distribution and genetic structure

Brown troutSalmo truttaL. lives mainly in European rivers and is also bred in hatcheries for fishery purposes. Since the end of 19th century it has been introduced in all other continents. For the present survey most of the known self-sustaining brown trout river populations in Japan have been sampled and analyzed through sequences of the entire mitochondrial DNA control region and twelve microsatellites. In Japan, brown trout are genetically not homogeneous, probably as a consequence of several introductions, one in the Azusa river and at least one other in the remaining territory. The Chuzenji hatchery houses a genetically very distinct strain, probably due to intense manipulation in isolated scientific experimentations over 30 years. Finally, most populations showed high genetic diversity (Mamachi, Kane and Odori streams, Lake Chuzenji) with the exception of the Azusa river samples. This molecular analysis clearly demonstrates a European north Atlantic origin arrived in two distinct ways.

Mitochondrial DNA variation in Sub-Saharan Africa: Forensic data from a mixed West African sample, Côte d’Ivoire (Ivory Coast), and Rwanda

This study provides 398 novel complete mitochondrial control region sequences that augment the still underrepresented data from Africa by three datasets: a mixed West African sample set deriving from 12 countries (n = 145) and datasets from Côte d’Ivoire (Ivory Coast) (n = 100) as well as Rwanda (n = 153). The analysis of mtDNA variation and genetic comparisons with published data revealed low random match probabilities in all three datasets and typical West African and East African diversity, respectively. Genetic parameters indicate that the presented mixed West African dataset may serve as first forensic mtDNA control region database for West Africa in general. In addition, a strategy for responsible forensic application of precious mtDNA population samples potentially containing close maternal relatives is outlined. The datasets will be uploaded to the forensic mtDNA database EMPOP (https://empop.online) upon publication.

Demographic history and population genetic analysis of Decapterus maruadsi from the northern South China Sea based on mitochondrial control region sequence.

Late Pleistocene climate oscillations are believed to have greatly influenced the distribution, population dynamics, and genetic variation of many marine organisms in the western Pacific. However, the impact of the late Pleistocene climate cycles on the demographic history and population genetics of pelagic fish in the northern South China Sea (SCS) remains largely unexplored. In this study, we explored the demographic history, genetic structure, and genetic diversity of Decapterus maruadsi, a typical pelagic fish, over most of its range in the northern SCS. A 828–832 bp fragment of mitochondrial control region were sequenced in 241 individuals from 11 locations. High haplotype diversity (0.905–0.980) and low nucleotide diversity (0.00269–0.00849) was detected, revealing low levels of genetic diversity. Demographic history analysis revealed a pattern of decline and subsequent rapid growth in the effective population size during deglaciation, which showed that D. maruadsi experienced recent demographic expansion after a period of low effective population size. Genetic diversity, genetic structure, and phylogenetic relationship analysis all demonstrated that no significant genetic differentiation existed among the populations, indicating that D. maruadsi was panmictic throughout the northern SCS. Periodic sea-level changes, fluctuation of the East Asian Monsoon, and Kuroshio variability were responsible for the population decline and expansion of D. maruadsi. The demographic history was the primary reason for the low levels of genetic diversity and the lack of significant genetic structure. The life history characteristics and ocean currents also had a strong correlation with the genetic homogeneity of D. maruadsi. However, the genetic structure of the population (genetic homogeneity) is inconsistent with biological characteristics (significant difference), which is an important reminder to identify and manage the D. maruadsi population carefully.

Genetic structure of Mexican lionfish populations in the southwest Gulf of Mexico and the Caribbean Sea.

The recent expansion of the invasive lionfish throughout the Western Hemisphere is one of the most extensively studied aquatic invasions. Molecular studies have improved our understanding of larval dispersal, connectivity, and biogeographical barriers among lionfish populations, but none have included Mexican localities, an important area for the larval dispersal of Pterois volitans through the Western Caribbean and the Gulf of Mexico. Here, we present a genetic analysis of lionfishes collected along Mexican coasts, examining their connectivity with other Caribbean localities (Belize, Cuba, Puerto Rico) and the role of ocean currents on population structure. We collected 213 lionfish samples from seven locations comprising four countries. To evaluate genetic structure, mitochondrial control region and nuclear inter-simple sequence repeat markers were used. We found that lionfish collected along Mexican coasts show a similar haplotype composition (H02 followed by H01 and H04) to other Caribbean locations, and the H03 rare haplotype was not found. Haplotype composition in the southwest Gulf of Mexico suggests a discontinuity between the southern and northern areas of the Gulf of Mexico. The southern area clustered more strongly to the Caribbean region, and this is supported by the complexity of water circulation in the semi-enclosed region of the Gulf of Mexico. Mitochondrial genetic diversity parameters show small values, whereas nuclear markers produce medium to high values. Only nuclear markers highlighted significant genetic differentiation between the southwest Gulf of Mexico and Caribbean region, confirming a phylogeographic break between both regions. Separate analysis of Caribbean locations indicates restricted larval exchange between southern and northern regions of the Mesoamerican Barrier Reef System, potentially in response to regional oceanographic circulation.

The First Molecular Evidence of Korean Zalophus japonicus (Otariidae: Sea Lions) from the Archaeological Site of Dokdo Island, Korea

Zalophus japonicus (Japanese sea lion, family Otariidae) was a mammal that once flourished around Dokdo Island. Overharvesting of the Korean sea lion in the early and mid-20th century resulted in a drastic decline of individual numbers, and it is currently listed as an extinct species by the International Union for Conservation of Nature (IUCN). An attempt is made to analyze the DNA sequences of the Korean sea lion with Japanese samples and living sea lions in the context of modern biology. Bones of Z. japonicus were retrieved from the archaeological site in Dokdo Island, and DNA sequences of mitochondrial control region (Dloop) were isolated using molecular methods. The DNA sequences of Korean Z. japonicus showed a high sequence similarity (98–99%) but did not exactly match with those reported from bone samples of stuffed specimens of the Japanese Z. japonicus caught in Japanese territories. As expected, the mitochondrial sequence was clearly distinct from two other sea lions, Z. californianus and Z. wollebaeki (92–93%). This is the first molecular identification of the Korean Z. japonicus and could provide useful information for species identification and genetic diversity of Z. japonicus. We believe that this key reference can play a significant role in the recovery of natural populations of Z. japonicus.

First record of false killer whales (Pseudorca crassidens) in the Falkland Islands (Malvinas)

The false killer whale (Pseudorca crassidens) is primarily distributed across tropical, subtropical and warm temperate waters, with few records originating above 50° latitude in each hemisphere. In February 2013, a mass stranding of 22 false killer whales occurred on the east coast of the Falkland Islands (Malvinas; 51.83°S, 58.24°W). Of the 20 sexed animals, 11 were male and 9 were female. Total body lengths ranged from 396 to 581 cm, and the stranded animals likely consisted entirely of mature adults. There were no significant differences between the sexes in proportional body measurements, with the exception of proportional dorsal fin height which was significantly higher in males. Tooth counts ranged from 14 to 18 in the upper jaws, and from 14 to 20 in the lower jaws. Four stomachs were investigated, of which three were empty and one contained a single Onychoteuthidae squid (Onykia ingens) beak. Mitochondrial control region sequences from the stranded animals indicated greater genetic connectivity between the south Pacific and south Atlantic than between the south and north Atlantic ocean basins. Given the absence of full necropsies, the underlying reasons for the stranding could not be ascertained. This mass stranding represents the first confirmed record of false killer whales in the Falkland Islands, and provides new information on the species in the southernmost part of its distributional range.

Cryptic species and independent origins of allochronic populations within a seabird species complex (Hydrobates spp.)

Humans are inherently biased towards naming species based on morphological differences, which can lead to reproductively isolated species being mistakenly classified as one if they are morphologically similar. Recognising cryptic diversity is needed to understand drivers of speciation fully, and for accurate estimates of global biodiversity and assessments for conservation. We investigated cryptic species across the range of band-rumped storm-petrels (Hydrobates spp.): highly pelagic, nocturnal seabirds that breed on tropical and sub-tropical islands in the Atlantic and Pacific Oceans. In many breeding colonies, band-rumped storm-petrels have sympatric but temporally isolated (allochronic) populations; we sampled all breeding locations and allochronic populations. Using mitochondrial control region sequences from 754 birds, cytochrome b sequences from 69 birds, and reduced representation sequencing of the nuclear genomes of 133 birds, we uncovered high levels of genetic structuring. Population genomic analyses revealed up to seven unique clusters, and phylogenomic reconstruction showed that these represent seven monophyletic groups. We uncovered up to six independent breeding season switches across the phylogeny, spanning the continuum from genetically undifferentiated temporal populations to full allochronic species. Thus, band-rumped storm-petrels encompass multiple cryptic species, with non-geographic barriers potentially comprising strong barriers to gene flow.

Noninvasive DNA sampling and camera trapping suggest dramatic regional conservation status of an understudied carnivore: the Rüppell’s fox in Tunisia

ABSTRACTRüppell’s fox, Vulpes rueppellii, is one of the four fox species occurring in North Africa. Its population status and ecology remains largely unknown. Here, we collected occurrence data from camera trapping and scat-collection based mitochondrial control region sequencing to assess the distribution range and status of the species across potential habitats in Tunisia. The collection and analysis of 342 scat samples resulted in 234 sequences of the mitochondrial control region. Our results did not reveal any evidence of Rüppell’s fox presence in Tunisia. In contrast, three other mesocarnivores were commonly recorded by camera trapping and molecular data, namely African wolf ‘Canis lupaster’, red fox ‘Vulpes vulpes’ and fennec fox ‘V. zerda’. The three species exhibited distinct geographical affinities, which are reflected in different habitat selection patterns. To the best of our knowledge, this is the first study focusing on the distribution of V. rueppellii in North Africa using both camera trapping and noninvasive genetic methods. In terms of conservation, it seems urgent to characterise the status of this species in North Africa, and particularly in Tunisia.

Genetic identification of native populations of Mediterranean brown trout Salmo trutta L. complex (Osteichthyes: Salmonidae) in central Italy

Italian native populations of Mediterranean brown trout belong to the Salmo trutta complex. This species complex includes many mitochondrial lineages and phenotypes that have caused taxonomic controversies over time. The spatial distribution and the genetic diversity of these fishes are threatened by habitat destruction, global warming and, mainly, by the introduction of domestic trout of Atlantic origin. Indeed allochthonous trouts were massively restocked in Italian rivers for a century and they admixed with native populations. In order to identify residual native populations of Mediterranean brown trout, a genetic analysis of specimens collected within Latium region, on the Tyrrhenian slope of central Italy, was undertaken. To this purpose, 210 trout specimens were collected from six different rivers and analyzed for the identification of their nuclear (LDH-C1* RFLP) and mitochondrial (Control Region sequences) genotypes. Genetic characterization with these molecular markers allowed a quantitative estimate of allochthonous genotypes, which are present in all brown trout populations of the six sites, even if not equally distributed across the sampling area. At least three populations, inhabiting diverse lotic ecosystems (mountain, hilly and coastal streams respectively), are characterized by a high percentage of native nuclear allele *100 at locus LDH-C1* and typical Mediterranean haplotypes (of AD and ME lineages), which can be considered as different management units (MUs). This finding highlighted the aquatic ecosystems of the Latium Region as an important hotspot of salmonid biodiversity within the Italian peninsula, with important implications from a conservation perspective.

Dual DNA-protein extraction from human archeological remains

Human skeletal remains may be considered bio-archives due to their particular combination of mechanical, structural, and chemical properties that render natural resistance against post-mortem degradation of ancient biomolecules. The survival of organic matter in ancient tissues is of great interest due to its potential in recovering information on the historical past of individuals and populations including health, dietary history, ancestry, and migration patterns. Even though the ancient biomolecules have become a powerful research tool, the archeogenetic research field can often deal with obstacles regarding the limited availability of osteological material and/or ethical concerns as their analysis is destructive. Here, we describe an alternative, efficient method for simultaneous extraction of DNA and proteins from the same archeological sample source, thus limiting the damage to valuable ancient human skeletal remains. The proposed method consists of overnight decalcification of powdered tissue, purification and concentration of biomolecules, and separation of the resulting solution for subsequent DNA purification and protein precipitation. Its performance was assessed relative to previously described approaches, comparing the concentration of the retrieved biomolecules. Our results show that this method designed to co-purify DNA and proteins is appropriate to obtain authentic sequences of the human mitochondrial control region from medieval or more recent human teeth. Also, the resulting proteins can be used for immunochromatographic detection of malaria in skeletal material suspect of infection with Plasmodium sp.

Genetic connectivity and phylogeography of the night shark (Carcharhinus signatus) in the western Atlantic Ocean: Implications for conservation management

Abstract The night shark, Carcharhinus signatus, is a mesopelagic, semi‐oceanic shark species found only in the Atlantic Ocean. It is one of the most frequently caught sharks in pelagic longline fisheries and is classified as Vulnerable by the International Union for the Conservation of Nature (IUCN). Despite their prevalence in commercial fisheries, the population genetic structure of the night shark has not been assessed. The present study investigated the genetic diversity, genetic connectivity, and phylogeography of the species throughout the western Atlantic Ocean, based on complete mitochondrial control region (mtCR) sequence data (n = 152) and genotypic data from nine nuclear microsatellites (n = 119). The mtCR sequence revealed 19 haplotypes, with overall haplotype and nucleotide diversities of 0.74 (±0.027) and 0.0034 (±0.0019), respectively, whereas the nuclear microsatellite observed and expected heterozygosities were 0.408 and 0.421, respectively. There was significant population structure (ФST = 0.429; P < 0.01) and isolation by distance (r = 0.65, P = 0.03) based on mtCR sequence data, but no genetic differentiation based on nuclear microsatellite analyses. The phylogenetic analyses support the existence of two matrilineal lineages, which diverged during the Pleistocene. Mitochondrial demographic analyses indicated a historical bottleneck effect followed by population expansion during the Pleistocene, whereas nuclear microsatellites did not detect a recent or a strong bottleneck. For conservation purposes, we advocate that the species should be considered to comprise at least two management units (MUs) in the western Atlantic Ocean. MU‐specific catch quotas should be implemented throughout the range of the species given its low genetic diversity and vulnerability to overexploitation.

Population genetics of the bigeye thresher shark Alopias superciliosus in the Atlantic and Indian Oceans: implications for conservation

Population structure and genetic connectivity are pivotal contributions to the establishment of conservation strategies for fisheries management, in particular for highly migratory species that are affected by commercial fisheries. This study used partial sequences of mitochondrial DNA control region to determine the genetic structure of the bigeye thresher shark Alopias superciliosus in the Atlantic and Indian Oceans. A total of 858 base pairs of mtDNA CR from 228 individuals were analyzed. The resulting nucleotide diversity (π) was 0.0011 ± 0.0008 and the haplotype diversity (h) was 0.127 ± 0.030. These are the lowest diversities registered in elasmobranchs with this genetic marker. Two genetically distinct lineages were identified, one of them represented by 3.9% of the analyzed individuals and none restricted to any particular area. Simulated scenarios of population structure, tested with AMOVA and pairwise ΦST did not result in significant values indicating high connectivity among all sampled groups. The absence of population structure, even between Atlantic and Indian Oceans, corroborates the high dispersal ability of this species. The low genetic diversity detected in this species and the identification of two historical lineages occurring in sympatry, one represented by a very small number of individuals, should be considered in the conservation efforts and management plans of A. superciliosus.

Moderate genetic variability and no genetic structure within the European golden jackal (Canis aureus) population in Hungary

Demography of the golden jackal (Canis aureus) was affected by various events in the past, but today jackal populations are increasing throughout Europe. Despite the fact that it is one of the most rapidly spreading mammals in Europe, previous genetic studies detected low genetic diversity among and within populations. The Hungarian landscape is not highly varied; however, it is in the middle of the country’s territory that the jackal’s number is significantly increasing. Therefore, the main goal of our research was to further investigate the genetic diversity and population structure of the Hungarian golden jackal population based on a larger sample size than in previous studies ever, expecting that individuals from genetically differentiated subpopulations might meet in the area studied. Seventy golden jackals from the most populated area, Western Hungary, were studied with regard to genetic variability, differentiation, and structure as revealed by 385-bp-long mitochondrial control region sequences and 10 nuclear canine microsatellite loci. There was no variation at all in the mtDNA CR sequences, and nuclear variability was low (average observed and expected heterozygosity of 0.348 and 0.447, respectively). Furthermore, no obvious genetic structuring was detected in the studied population using GENELAND and PCA analyses. The present regional genetic structure and diversity of the Hungarian golden jackal is consistent with the previous results; however, it is the first analysis based on a relatively large sample size. We concluded that further molecular genetic studies are needed with a more specific marker set to have more accurate knowledge on rate of hybridization and genetic structure in golden jackal populations across Hungary and Europe.

Comparison of the rookery connectivity and migratory connectivity: insight into movement and colonization of the green turtle (Chelonia mydas) in Pacific–Southeast Asia

Integration of the rookery connectivity, which includes historical connections among rookeries, and migratory connectivity assessing dispersal or migratory routes of marine animals are important for understanding dispersal and/or migration and its effect on the formation of genetic population structure. The migratory nature and long-distance movement of sea turtles have been reported, while natal philopatry has been suggested by genetic differentiation among rookeries within a relatively narrow geographic scale. Therefore, we hypothesize that contemporary long-distance movement has a limited effect on colonization in new rookeries. This study compared the genetic relationships among rookeries and between the rookeries and foraging grounds of green turtles (Chelonia mydas) in Southeast Asia. Mitochondrial control region sequences of 333 turtles from 11 rookeries were newly determined, and combination with previously reported Indo-Pacific rookeries indicated the presence of a genetic barrier in the Torres Strait and Celebes Sea (i.e. Philippines–Sulawesi). On the other hand, an analysis of newly collected 107 turtles from seven foraging sites and mixed stock analyses indicated contemporary movement across this historical genetic barrier, from Micronesian rookeries to foraging grounds in the Celebes Sea (i.e. Sipadan Island and Tun Sakaran Marine Park). Isolation by distance was generally supported for relationships among rookeries, and the high migratory connectivity did not result in a lower genetic distance between rookeries than predicted from geographic distance. Differences between rookery connectivity and migratory connectivity in green turtles in Southeast Asia are likely due to migration to natal regions after long-distance movement.

How sea level change mediates genetic divergence in coastal species across regions with varying tectonic and sediment processes.

Platetectonics and sediment processes control regional continental shelf topography. We examine the genetic consequences of how glacial-associated sea level change interacted with variable nearshore topography since the last glaciation. We reconstructed the size and distribution of areas suitable for tidal estuary formation from the last glacial maximum, ~20 thousand years ago, to present from San Francisco, California, USA (~38°N) to Reforma, Sinaloa, Mexico (~25°N). We assessed range-wide genetic structure and diversity of three codistributed tidal estuarine fishes (California Killifish, Shadow Goby, Longjaw Mudsucker) along ~4,600km using mitochondrial control region and cytB sequence, and 16-20 microsatellite loci from a total of 524 individuals. Results show that glacial-associated sea level change limited estuarine habitat to few, widely separated refugia at glacial lowstand, and present-day genetic clades were sourced from specific refugia. Habitat increased during postglacial sea level rise and refugial populations admixed in newly formed habitats. Continental shelves with active tectonics and/or low sediment supply were steep and hosted fewer, smaller refugia with more genetically differentiated populations than on broader shelves. Approximate Bayesian computation favoured the refuge-recolonization scenarios from habitat models over isolation by distance and seaway alternatives, indicating isolation at lowstand is a major diversification mechanism among these estuarine (and perhaps other) coastal species. Because sea level change is a global phenomenon, we suggest this top-down physical control of extirpation-isolation-recolonization may be an important driver of genetic diversification in coastal taxa inhabiting other topographically complex coasts globally during the Mid- to Late Pleistocene and deeper timescales.

Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers.

The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being "near threatened", current understanding of habitat use and population structure of Carcharhinus galapagensis is limited to specific areas within its distribution. We evaluated population structure and connectivity across the Pacific Ocean using genome-wide single-nucleotide polymorphisms (~7200 SNPs) and mitochondrial control region sequences (945 bp) for 229 individuals. Neutral SNPs defined at least two genetically discrete geographic groups: an East Tropical Pacific (Mexico, east and west Galapagos Islands), and another central-west Pacific (Lord Howe Island, Middleton Reef, Norfolk Island, Elizabeth Reef, Kermadec, Hawaii and Southern Africa). More fine-grade population structure was suggested using outlier SNPs: west Pacific, Hawaii, Mexico, and Galapagos. Consistently, mtDNA pairwise ΦST defined three regional stocks: east, central and west Pacific. Compared to neutral SNPs (FST = 0.023-0.035), mtDNA exhibited more divergence (ΦST = 0.258-0.539) and high overall genetic diversity (h = 0.794 ± 0.014; π = 0.004 ± 0.000), consistent with the longstanding eastern Pacific barrier between the east and central-west Pacific. Hawaiian and Southern African populations group within the west Pacific cluster. Effective population sizes were moderate/high for east/west populations (738 and 3421, respectively). Insights into the biology, connectivity, genetic diversity, and population demographics informs for improved conservation of this species, by delineating three to four conservation units across their Pacific distribution. Implementing such conservation management may be challenging, but is necessary to achieve long-term population resilience at basin and regional scales.

Phylogeography of screaming hairy armadillo Chaetophractus vellerosus: Successive disjunctions and extinctions due to cyclical climatic changes in southern South America.

Little is known about phylogeography of armadillo species native to southern South America. In this study we describe the phylogeography of the screaming hairy armadillo Chaetophractus vellerosus, discuss previous hypothesis about the origin of its disjunct distribution and propose an alternative one, based on novel information on genetic variability. Variation of partial sequences of mitochondrial DNA Control Region (CR) from 73 individuals from 23 localities were analyzed to carry out a phylogeographic analysis using neutrality tests, mismatch distribution, median-joining (MJ) network and paleontological records. We found 17 polymorphic sites resulting in 15 haplotypes. Two new geographic records that expand known distribution of the species are presented; one of them links the distributions of recently synonimized species C. nationi and C. vellerosus. Screaming hairy armadillo phylogeographic pattern can be addressed as category V of Avise: common widespread linages plus closely related lineages confined to one or a few nearby locales each. The older linages are distributed in the north-central area of the species distribution range in Argentina (i.e. ancestral area of distribution). C. vellerosus seems to be a low vagility species that expanded, and probably is expanding, its distribution range while presents signs of genetic structuring in central areas. To explain the disjunct distribution, a hypothesis of extinction of the species in intermediate areas due to quaternary climatic shift to more humid conditions was proposed. We offer an alternative explanation: long distance colonization, based on null genetic variability, paleontological record and evidence of alternance of cold/arid and temperate/humid climatic periods during the last million years in southern South America.

Small marsupial, big dispersal? Broad- and fine-scale genetic structure of an endangered marsupial from the Australian arid zone

The irregular nature of rainfall in the Australian arid and semiarid zones results in a heterogeneous distribution of resources in both time and space. The mammal species that reside in these regions are uniquely adapted to these climatic conditions, often occurring in naturally low densities and increasing significantly in numbers following major rainfall events. We investigated how these adaptations may influence genetic diversity and gene flow across the landscape in an endangered semiarid/arid-zone marsupial, the sandhill dunnart (Sminthopsis psammophila), from three known populations in southern Australia. Analyses of mitochondrial control region (CR) sequences and microsatellite loci revealed that S. psammophila had maintained similar levels of genetic diversity to other sympatric Sminthopsis species despite its endangered status. There was no evidence for significant phylogeographic structure within the species, but each population was genetically differentiated, based on the frequency of microsatellite alleles and CR haplotypes, suggesting that they should be considered as distinct Management Units for conservation. At a fine spatial scale, no significant genetic structure or sex-biased dispersal was detected within a study site of 240km2. These findings suggest that both sexes are highly mobile, which allows individuals to locate localised resource patches when they become available. We detected evidence of a genetic bottleneck within the population, possibly caused by a recent drought. Our study highlights the importance of maintaining connectivity across the landscape for semiarid- and arid-zone species to enable them to track resource pulses and maintain genetic diversity.

Effects of Pleistocene glaciation on the phylogeographic and demographic histories of chub mackerel Scomber japonicus in the north-western Pacific

Pleistocene glacial cycles associated with geological and climatic changes have been suggested to affect the distribution and abundance of marine organisms in the north-western Pacific. In addition to historical processes, several contemporary forces are associated with spatial distributions and genetic structuring of marine species. Herein, we gathered partial mitochondrial control region sequences of chub mackerel Scomber japonicus from 14 localities over most of its geographical range in the north-western Pacific to infer the effect of Pleistocene climatic fluctuations on its historical demography, and to assess the role of historical process and contemporary factors in shaping present-day patterns of genetic differentiation within this species. Phylogeographic patterns revealed two distinct lineages that originated in vicariance during the Middle Pleistocene. However, there was no evidence of phylogeographic partitioning of haplotypes over the sampled range. Population structure analyses indicated a high degree of genetic homogeneity among chub mackerel populations. Demographic analyses indicated both lineages experienced Late Pleistocene population expansion. The observed genetic pattern of chub mackerel is consistent with a scenario of the survival of this species in at least two allopatric glacial refugia during the glacial maxima of the Pleistocene followed by massive dispersals throughout the north-western Pacific and species-specific ecological processes facilitating contemporary gene flow.

Genetic Diversity of an Imperiled Neotropical Catfish and Recommendations for Its Restoration.

The long-whiskered catfish Steindachneridion parahybae (Family Pimelodidae) is endemic to the Paraíba do Sul River basin in southeastern Brazil. This species was heavily exploited by artisanal fisheries and faces challenges posed by dams, introduced species, and deterioration of critical habitat. The remaining populations are small and extirpated from some locales, and the species is listed as critically endangered in Brazil. Screening variation at a partial mitochondrial control region sequence (mtCR) and 20 microsatellite loci, we: (i) describe the patterns of genetic diversity along its current distributional range; (ii) test the null hypothesis of panmixia; (iii) investigate the main factors driving its current population structure, and (iv) propose management of broodstock for fostering recovery of wild populations through genetically cognizant restocking. Our microsatellite data for 70 individuals from five collections indicate moderate levels of heterozygosity (HO = 0.45) and low levels of inbreeding (FIS = 0.016). Individual-based cluster analyses showed clear genetic structure, with three clusters of individuals over the collection area with no mis-assigned individuals, suggesting no recent migration among the three clusters. Pairwise DEST values showed moderate and significant genetic differentiation among all populations so identified. The MUR population may have suffered a recent demographic reduction. mtCRs for 70 individuals exhibited 36 haplotypes resulting from 38 polymorphic sites. Overall, mitochondrial haplotype diversity was 0.930 (±0.023) and nucleotide diversity was 0.011 (±0.002). Significant population structure was observed, with ϕST = 0.226. Genetic markers could be used in a hatchery-based restoration program emphasizing breeding of pairs with low kinship values in order to promote retention of genetic diversity and avoid inbreeding. Individual average kinship relationships showed 87.3% advised matings, 11.0% marginal matings, and 1.7% advised against. While these results comprise a contribution toward planning better breeding management and monitoring, parallel actions to be undertaken include surveying healthy riverine habits for reintroduction and continued searching for wild individuals to introduce new variation into the captive broodstock to avoid adaptation to captivity and to minimize inbreeding.