Genetic diversity of the endangered endemic Agave victoriae-reginae (Agavaceae) in the Chihuahuan Desert

Long-lived perennials are a species-rich, ecologically important component of the North American deserts, yet we know little about their genetic structure, information important for their conservation. Agave victoriae-reginae is an endemic of the Chihuahuan Desert of northern Mexico that is endangered by collection for the ornamental trade. We examined levels and patterns of variation at ten polymorphic allozyme loci in ten populations representing the range of the species. Levels of genetic variation (mean H_e= 0.335) and differentiation (mean F_ST = 0.236) were high. Phenetic clustering suggested the existence of at least three distinct groups of populations. If this pattern of variation is representative of other long-lived desert perennials, it may explain the species richness of this group and will pose a real challenge to gene conservation efforts.     

Post-glacial colonization of brown trout, Salmo trutta L.: Ldh-5 as a phylogeographic marker locus

The Ldh-5 locus, which codes for the eye-specific lactate dehydrogenase in brown trout, has been shown to be polymorphic for two codominant alleles, Ldh-5 (100) and Ldh-5 (90). The Ldh-5 (100 ) allele is present in 11 other salmonid species and is therefore likely to be the ancestral one, whereas the unique brown trout Ldh-5 (90 ) allele would seem to be the result of a mutation in that lineage. The Ldh-5 (90 ) allele appears to have arisen in north-west Europe during or after the last glaciation, with allelic substitution taking place under the action of natural selection. The Ldh-5 (90 ) allele can be used as a phylogeographic marker to trace the post-glacial spread of the populations possessing it. Examination of the current distribution of the two alleles suggests that, in the formerly glaciated area of north-west Europe, there have been two post-glacial colonizations by brown trout. The first was by an 'ancestral' race fixed for the Ldh-5(100 ) allele. This was later replaced by, or introgressed with, the later-arriving 'modern' race characterized by the Ldh-5 (90 ) allele, except where physical barriers prevented colonization by this latter form. Artificial stocking has resulted in 'genetic contamination' of many populations of the ancestral race and there is an urgent need to conserve the remaining pristine populations, especially in view of the likely genetic propensity for longevity and ultimate large size exhibited by this race.     

Characterization of transferrin‐linked microsatellites in brown trout (Salmo trutta) and Atlantic salmon (Salmo salar)

The transferrin (TF) gene has recently received increased interest in fish given its fitness relevance as a resistance gene against pathogenic bacteria. In this study, we characterized five TF‐linked microsatellites in brown trout (Salmo trutta) and Atlantic salmon (Salmo salar). Interestingly, each marker amplified duplicated loci and linkage analysis revealed that the TF gene has most likely experienced a tandem duplication during salmonid evolution. In addition, the amplification of all five markers across a wide range of salmonid species suggests that they may be of general interest for the genetic analysis of the TF gene(s) in this teleost family.     

Dynamic micro-geographic and temporal genetic diversity in vertebrates: the case of lake-spawning populations of brown trout (Salmo trutta)

Conservation of species should be based on knowledge of effective population sizes and understanding of how breeding tactics and selection of recruitment habitats lead to genetic structuring. In the stream‐spawning and genetically diverse brown trout, spawning and rearing areas may be restricted source habitats. Spatio–temporal genetic variability patterns were studied in brown trout occupying three lakes characterized by restricted stream habitat but high recruitment levels. This suggested non‐typical lake‐spawning, potentially representing additional spatio–temporal genetic variation in continuous habitats. Three years of sampling documented presence of young‐of‐the‐year cohorts in littoral lake areas with groundwater inflow, confirming lake‐spawning trout in all three lakes. Nine microsatellite markers assayed across 901 young‐of‐the‐year individuals indicated overall substantial genetic differentiation in space and time. Nested gene diversity analyses revealed highly significant (≤P = 0.002) differentiation on all hierarchical levels, represented by regional lakes (F_LT = 0.281), stream vs. lake habitat within regional lakes (F_HL = 0.045), sample site within habitats (F_SH = 0.010), and cohorts within sample sites (F_CS = 0.016). Genetic structuring was, however, different among lakes. It was more pronounced in a natural lake, which exhibited temporally stable structuring both between two lake‐spawning populations and between lake‐ and stream spawners. Hence, it is demonstrated that lake‐spawning brown trout form genetically distinct populations and may significantly contribute to genetic diversity. In another lake, differentiation was substantial between stream‐ and lake‐spawning populations but not within habitat. In the third lake, there was less apparent spatial or temporal genetic structuring. Calculation of effective population sizes suggested small spawning populations in general, both within streams and lakes, and indicates that the presence of lake‐spawning populations tended to reduce genetic drift in the total (meta‐) population of the lake.     

Heterozygote excess in ancient populations of the critically endangered Dioon caputoi (Zamiaceae,Cycadales) from central Mexico

Dioon caputoi is a long‐lived cycad known from only four populations that range in size from 50 to 120, mostly adult individuals. Dioon caputoi has the most narrow geographical range of all Dioon spp. (less than 10 km), existing completely within the boundaries of the Tehuacán–Cuicatlán Biosphere Reserve, Mexico. Negative inbreeding values were found in all four populations (F_IT = ?0.242) and within subpopulations (F_IS = ?0.379). Only c. 10% of the total genetic variation was partitioned among populations (F_ST = 0.099). We also found that most mean values of genetic variation (A = 1.91 ± 0.12; P = 78.9 ± 10.2; H_E = 0.35 ± 0.01) are within the range reported for other Dioon species with larger populations and with wider geographical ranges. These results support recent findings that rare plant species maintain high levels of genetic diversity. The heterozygote excess found at all loci is discussed in detail from a neutral evolutionary perspective, leaving arguments as working hypotheses for further research. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158 , 436–447.     

Genetic differentiation among the sympatric brown trout (Salmo trutta) populations of Lough Melvin, Ireland

Three morphotypes of brown trout have been described from Lough Melvin in north-west Ireland: gillaroo; sonaghen; ferox. The extensive genetic differences among the three types indicate that they are reproductively isolated, i.e. separate stocks of trout. For example, only gillaroo possess the Ldh -1(n) allele. Ferox show a high frequency of the Ldh -5(100) allele and this allele does not exceed a frequency of 0.02 in the other two types. Sonaghen are characterized by relatively much higher frequencies for Ck -2(115) and Gpi- 2(135) alleles. Sampling over a period of 7 years and experiments with artificial stocks of gillaroo and sonaghen have demonstrated that these differences are temporally stable. On the basis of observation of mature adults and the genetic composition of fry samples, it has been shown that the three types maintain their genetic integrity as the result of their distinctive spawning habits with gillaroo spawning in the lake and outflowing river, sonaghen in the smaller inflowing rivers and ferox in the deep downstream section of the largest inflowing river. The ferox is a relict population of an early post-glacial trout colonist while gillaroo and sonaghen are representative of a more recent independent colonization. However, it cannot be determined at present whether or not gillaroo and sonaghen were already differentiated prior to colonizing Melvin although the weight of evidence favours a sympatric split. It is proposed that the three types of trout be designated as separate subspecies to highlight the need for independent management and urgent requirement for conservation action.     

Extreme genetic differentiation among the remnant populations of marble trout (Salmo marmoratus) in Slovenia

Populations of the marble trout (Salmo marmoratus) have declined critically due to introgression by brown trout (Salmo trutta) strains. In order to define strategies for long-term conservation, we examined the genetic structure of the 8 known pure populations using 15 microsatellite loci. The analyses reveal extraordinarily strong genetic differentiation among populations separated by < 15 km, and extremely low levels of intrapopulation genetic variability. As natural recolonization seems highly unlikely, appropriate management and conservation strategies should comprise the reintroduction of pure populations from mixed stocks (translocation) to avoid further loss of genetic diversity.     

The trout (Salmo trutta) population of the Afon Cwm, a small tributary of the Afon Dyfi, mid-Wales

Data are presented from a 10-year (1984 to 1993) study of a Salmo trutta population in the Afon Cwm, a small tributary of the Afon Dyfi, mid-Wales. The stream is a spawning and nursery area for sea trout. Growth of trout within the stream can be summarized by a von Bertalanffy growth coefficient ( K ) of 0·310, with asymptotic length (1∞) 21·6 cm and with length at age 1 of 7·6 cm. Mean population density in the whole stream varied from year to year between 0·05 and 0·60 0-group trout m⁻² and between 0·05 and 0·70 older trout m⁻². Mean biomass varied, between years, from 0·1 to 3·5 g m⁻² for 0-group and from 1·3 to 10·4g m⁻² for older trout. Loss between 3 and 5 months of age appeared to be proportionate at about 50 to 60% and instantaneous loss rate from 5 to 53 months of age varied from 0·04 to 0·10 month⁻¹ and was positively correlated with cohort number at 3 months of age. Production between 3 and 53 months of age varied between cohorts from 3 to 8 g m ⁻² live weight.     

Effects of sea trout stocking on the population genetics of landlocked brown trout, Salmo trutta L., in the Conwy River system, North Wales, U.K.

The effect of the introduction of fry of anadromous sea trout, Salmo trutta L., on the genetic integrity of landlocked brown trout populations was evaluated. Samples were taken from six brown trout populations from streams above impassable waterfalls in the Conwy river system (North Wales, U.K.) in 1989 and 1990. Three of these streams had no known stocking history and three had been stocked with sea trout fry from the lower Conwy system over the last few years. Representatives of these sea trout were collected from two streams in the lower Conwy system and from a hatchery. Allele frequencies at 13 loci, six of which were polymorphic, were determined by starch gel electrophoresis.
The stocked populations were intermediate in their allele frequencies between unstocked brown trout and sea trout samples. A principal component analysis suggested significant numbers of hybrids in all of the stocked streams. This shows that some of the introduced sea trout did not migrate down the falls to the sea, but stayed in fresh water and hybridized with the local population. The significance of this finding for the conservation of the genetic resource of brown trout stocks is discussed.     

Beaufort trout MicroPlex: a high‐throughput multiplex platform comprising 38 informative microsatellite loci for use in resident and anadromous (sea trout) brown trout Salmo trutta genetic studies

A flexible panel consisting of 38 informative microsatellite markers for Salmo trutta is described. These markers were selected from a pool of over 150 candidate loci that can be readily amplified in four multiplex PCR groups but other permutations are also possible. The basic properties of each markers were assessed in six population samples from both the Burrishoole catchment, in the west of Ireland, and Lough Neagh, in Northern Ireland. A method to assess the relative utility of individual markers for the detection of population genetic structuring is also described. Given its flexibility, technical reliability and high degree of informativeness, the use of this panel of markers is advocated as a standard for S. trutta genetic studies.     

Effects of acute iron overload on Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss)

Distribution of radioiron to various tissues after intraperitoneal injections was examined in Atlantic salmon and rainbow trout. Liver and spleen were found to be the major iron storage tissues. Injections of 1 or 5 mg iron as ferric ammonium citrate led to a fall in hemoglobin levels in both species after 2 d. Hemoglobin levels returned to normal levels in rainbow trout after 8 d, but Atlantic salmon had not recovered, and Hb levels fell below 3 g/100 mL. In both species, the fall in Hb was associated with a raise in iron levels in spleen and liver, suggesting damage to erythrocytes. Atlantic salmon liver ferritin showed a two- to threefold increase, while rainbow trout showed a sixfold increase, and a more rapid response. The toxic effect of iron in fish appears to be different from the effect in other vertebrates.     

A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales

The rivers of southern England and northern France which drain into the English Channel contain several genetically unique groups of trout (Salmo trutta L.) that have suffered dramatic declines in numbers over the past 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 95 single nucleotide polymorphism (SNP) loci for trout from this region and investigate their applicability and variability in both target (i.e., southern English) and non-target trout populations from northern Britain and Ireland. In addition, we present three case studies which demonstrate the utility and resolution of these genetic markers at three levels of spatial separation:(a) between closely related populations in nearby rivers, (b) within a catchment and (c) when determining parentage and familial relationships between fish sampled from a single site, using both empirical and simulated data. The SNP loci will be useful for population genetic and assignment studies on brown trout within the UK and beyond.     

Recruitment as a driver of production dynamics in stream-resident brown trout (Salmo trutta)

1. The objective was to assess the role of recruitment as a determinant of the production dynamics of stream-resident brown trout ( Salmo trutta ) across replicate habitats of contrasting quality and population attributes. A total of 128-year-classes (YC) at 12 stream sites were examined along four tributaries of the Rio Esva drainage (northwestern Spain).
2. A meta-comparison revealed that growth, density, mortality and production were essentially site-specific. However, when all data were pooled, recruitment (as a delayed density-dependent process) affected both growth and mortality in a way such that individuals in YC with high recruitment grew less and had higher mortality.
3. The value of total YC production recorded covered the global range of variation in the production of stream salmonids reported in the literature. Linear regressions of log-transformed data revealed that 89.0%, 58.9% and 70.7% of the variation in YC density, biomass and production, respectively, were explained by variations in recruitment.
4. The inclusion of growth and mortality, together with recruitment, into a multiple regression increased the variance explained of the total YC production by 13.3%, from 70.7% to 84.0%.
5. The functional relationships between recruitment and the population attributes elucidated in this study appear to provide a useful tool for management applications, including forecasting population status.     

Microsatellite analysis of genetic population structure in an endangered salmonid: the coastal cutthroat trout (Oncorhynchus clarki clarki)

The genetic population structure of coastal cutthroat trout ( Oncorhynchus clarki clarki ) in Washington state was investigated by analysis of variation in allele frequencies at six highly polymorphic microsatellite loci for 13 anadromous populations, along with one outgroup population from the Yellowstone subspecies ( O. clarki bouvieri) (mean heterozygosity = 67%; average number of alleles per locus = 24). Tests for genetic differentiation revealed highly significant differences in genotypic frequencies for pairwise comparisons between all populations within geographical regions and overall population subdivision was substantial ( F _ST = 0.121, R _ST = 0.093), with 44.6% and 55.4% of the among-population diversity being attributable to differences between streams ( F _SR = 0.054) and between regions ( F _RT = 0.067), respectively. Analysis of genetic distances and geographical distances did not support a simple model of isolation by distance for these populations. With one exception, neighbour-joining dendrograms from the Cavalli-Sforza and Edwards' chord distances and maximum likelihood algorithms clustered populations by physiogeographic region, although overall bootstrap support was relatively low (53%). Our results suggest that coastal cutthroat trout populations are ultimately structured genetically at the level of individual streams. It appears that the dynamic balance between gene flow and genetic drift in the subspecies favours a high degree of genetic differentiation and population subdivision with the simultaneous maintenance of high heterozygosity levels within local populations. Results are discussed in terms of coastal cutthroat trout ecology along with implications for the designation of evolutionarily significant units pursuant to the US Endangered Species Act of 1973 and analogous conservation units.     

Conservation genetics of the endangered endemic Hawaiian genus Brighamia (Campanulaceae)

The endemic Hawaiian genus Brighamia (Campanulaceae) comprises two federally endangered, morphologically similar species, B. insignis from Kaua`i and Ni`ihau and B. rockii from Moloka`i. To assist the design of conservation management programs for these taxa, isozyme analyses were performed to assess the levels of genetic diversity at the population and species levels, including comparisons within and among seven natural populations and one ex situ collection each of B. insignis and B. rockii. Our sampling (N = 80) represents ~41% of all known individuals in the wild. Isozyme analyses revealed levels of genetic variation comparable to those reported for other Hawaiian flowering plant taxa but low levels of genetic variation at the population and species levels when compared to flowering plants in general. Ex situ individuals (N = 61) were genetically representative of natural populations and hence may appropriately serve as stock for population augmentations. The two morphologically similar Brighamia species were highly distinct genetically. The combination of morphological and ecological similarity with allozymic dissimilarity observed in Brighamia is unique among the Hawaiian taxa studied to date.     

New representatives of the genus Ancorabolina George, 2006 (Copepoda,Harpacticoida, Ancorabolidae) including remarks on ancorabolid phylogeny

Four new species of Ancorabolina George, 2006 (Copepoda: Harpacticoida: Ancorabolidae) are described: Ancorabolina belgicae sp. nov. (from the Porcupine Seabight, north‐east Atlantic Ocean), Ancorabolina anaximenesi sp. nov. and Ancorabolina galeata sp. nov. (both from Anaximenes Mountain, eastern Mediterranean Sea), and Ancorabolina divasecunda sp. nov. (from Cape and Guinea Basins, south‐east Atlantic Ocean). Furthermore, the generic diagnosis for Ancorabolina is provided and the position of the taxon within Ancorabolidae is discussed. The characters originally employed to allocate Ancorabolina to the subfamily Ancorabolinae Sars, 1909, are critically evaluated and two true autapomorphies for a monophyletic Ancorabolinae (including Ancorabolina) are recognized. Two autapomorphies supporting Ancorabolina are proposed: (1) cephalothorax posteriorly with pair of ventrolateral cuticular processes turned backwards and (2) loss of the third setal element subapically on the antennary endopod. The urgent need for a phylogenetic re‐evaluation of the paraphyletic subfamily Laophontodinae Lang, 1944 is stressed and evidenced by three characters widespread in this subfamily but also present in Ancorabolina. This may be an indication of a closer relationship of Ancorabolina with certain members of Laophontodinae. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 16–55.     

Genetic diversity and population structure of bocachico Prochilodus magdalenae (Pisces,Prochilodontidae) in the Magdalena River basin and its tributaries,Colombia

Prochilodus magdalenae is an endemic freshwater fish that occurs in the Magdalena, Sinú and Atrato hydrographic basins. It has an important economic role and is a food resource for the artisanal fishing communities. Its socioeconomic importance contrasts with the current status of its fisheries, where stocks are being depleted. Considering its importance and lack of information on its genetic structure, we used seven microsatellite markers to assess the genetic structure of wild populations of P. magdalenae. The genetic diversity was assessed and the population genetic structure was estimated through Fst, analysis of molecular variance and Bayesian analysis. A total of 290 alleles were found in all loci throughout all population. The high polymorphism contrasts with the levels of observed heterozygosity (Ho = 0.276), which are the lowest values recorded for the family. We found three populations of bocachico coexisting throughout the studied system, contradicting the hypothesis that freshwater migratory fish form panmictic populations. These results on the genetic structure of P. magdalenae constitute tools for a better understanding of the behavior and biology of this species, contributing to fish management and conservation programs.     

Mature male parr contribution to the effective size of an anadromous Atlantic salmon (Salmo salar) population over 30 years

We describe temporal changes in the genetic composition of a small anadromous Atlantic salmon (Salmo salar) population from South Newfoundland, an area where salmon populations are considered threatened (COSEWIC 2010). We examined the genetic variability (13 microsatellite loci) in 869 out‐migrating smolt and post‐spawning kelt samples, collected from 1985 to 2011 for a total of 22 annual collections and a 30 year span of assigned cohorts. We estimated the annual effective number of breeders (N_b) and the generational effective population size (N_e) through genetic methods and demographically using the adult sex ratio. Comparisons between genetic and demographic estimates show that the adult spawners inadequately explain the observed N_e estimates, suggesting that mature male parr are significantly increasing N_b and N_e over the study period. Spawning as parr appears to be a viable and important strategy in the near absence of adult males.     

Mitochondrial DNA differentiation between two forms of trout Salmo letnica, endemic to the Balkan Lake Ohrid, reflects their reproductive isolation

Mitochondrial haplotype diversity in sympatric populations of Ohrid trout, Salmo letnica was investigated by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the mtDNA control region and ND1, ND3/4, ND5/6 segments. A 310 bp fragment at the 5' end, and a 340-572 bp fragment at the 3' end of the control region were sequenced from representatives of the populations studied. Based on pairwise comparison of the sequences, five new haplotypes were identified plus one identical with the brown trout Andalusian haplotype from the southern Iberian Peninsula. The combination of both RFLP and sequence data sets yielded a total of 10 composite haplotypes. A high degree of genetic subdivision between S. letnica typicus and S. letnica aestivalis populations was observed. The notion of a sympatric origin for the two morphs is discussed. Length variation of the mtDNA control region due to the presence of an 82 bp unit, tandemly repeated one to four times, in the region between the conserved sequence block-3 (CSB-3) and the gene for phenylalanine tRNA is reported. Further, we demonstrate that a single duplication of the approximately 82 bp repeat unit is a common element of the salmonid mitochondrial control region. The unique genetic structure of Ohrid trout represents a highly valuable genetic resource that deserves appropriate management and conservation.     

Genetic diversity of trout (genus Salmo) from its most eastern native range based on mitochondrial DNA and nuclear gene variation

Russia and western Asia harbour trout populations that have been classified as distinct species and subspecies, most often on the basis of morphological and ecological variation. In order to assess their origins and to verify whether traditional taxonomy reflects their evolutionary distinctiveness, we documented their genetic relationships on the basis of mitochondrial DNA (mtDNA) RFLP, mtDNA sequence analysis, and allozyme variation. Both mtDNA and nuclear gene variation defined two ancient phylogenetic assemblages of populations distributed among northern (Baltic, White, Barents), and southern (Black, Caspian, Aral) sea basins, between which gene flow has been possible but limited in postglacial times. These results supported the traditional taxonomic differentiation between populations of these two regions. They provided weak support for the taxonomic distinction of southern brown trout (Salmo trutta) populations based on their basin of origin. They also refuted the hypothesis that L. Sevan trout (Salmo ischchan) diverged from a primitive brown trout ancestor. Nevertheless, all trout populations from southern sea basins possessed private alleles or mtDNA genotypes and were genetically distinct Therefore, they represent unique gene pools that warrant individual recognition for conservation and management.