Preserving genes, species, or ecosystems? Healing the fractured foundations of conservation policy

Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations

Simple Summary

In recent decades, societies, states and local authorities have become increasingly aware that for effective long-term management and protection of aquatic ecosystems and populations, it is necessary to take into account the genetic changes occurring in these populations. One type of high-resolution molecular marker suitable for studying the neutral and adaptive genetic diversity of populations is single nucleotide polymorphism (SNP). This review is an attempt to show the benefits of using SNPs to recognize natural populations of aquatic animals and detect the threats to them from accidentally or intentionally released farm animals, fishery and global climate changes. It is postulated that conservation actions should protect not only pristine natural populations that are endangered or overfished, but also protect populations of non-threatened species from unnecessarily released semi-domesticated animals. The enhancement of natural populations with farmed material usually reduces their genetic diversity. Experimental size-selective catches of artificially created populations have caused evolutionary changes in the life cycles of fishes. However, fishery-induced evolution in natural populations is difficult to observe. The negative measurable effects on populations can be expected when the number of breeding individuals is reduced below 100, which occurs very rarely in the sea and more often in fragmented freshwater streams, ponds and seasonal rivers.

Abstract

An increasing number of aquatic species have been studied for genetic polymorphism, which extends the knowledge on their natural populations. One type of high-resolution molecular marker suitable for studying the genetic diversity of large numbers of individuals is single nucleotide polymorphism (SNP). This review is an attempt to show the range of applications of SNPs in studies of natural populations of aquatic animals. In recent years, SNPs have been used in the genetic analysis of wild and enhanced fish and invertebrate populations in natural habitats, exploited migratory species in the oceans, migratory anadromous and freshwater fish and demersal species. SNPs have been used for the identification of species and their hybrids in natural environments, to study the genetic consequences of restocking for conservation purposes and the negative effects on natural populations of fish accidentally escaping from culture. SNPs are very useful for identifying genomic regions correlated with phenotypic variants relevant for wildlife protection, management and aquaculture. Experimental size-selective catches of populations created in tanks have caused evolutionary changes in life cycles of fishes. The research results have been discussed to clarify whether the fish populations in natural conditions can undergo changes due to selective harvesting targeting the fastest-growing fishes.

The paradox of retained genetic diversity of Hippocampus guttulatus in the face of demographic decline

Genetic diversity is the raw foundation for evolutionary potential. When genetic diversity is significantly reduced, the risk of extinction is heightened considerably. The long-snouted seahorse (Hippocampus guttulatus) is one of two seahorse species occurring in the North-East Atlantic. The population living in the Ria Formosa (South Portugal) declined dramatically between 2001 and 2008, prompting fears of greatly reduced genetic diversity and reduced effective population size, hallmarks of a genetic bottleneck. This study tests these hypotheses using samples from eight microsatellite loci taken from 2001 and 2013, on either side of the 2008 decline. The data suggest that the population has not lost its genetic diversity, and a genetic bottleneck was not detectable. However, overall relatedness increased between 2001 to 2013, leading to questions of future inbreeding. The effective population size has seemingly increased close to the threshold necessary for the population to retain its evolutionary potential, but whether these results have been affected by sample size is not clear. Several explanations are discussed for these unexpected results, such as gene flow, local decline due to dispersal to other areas of the Ria Formosa, and the potential that the duration of the demographic decline too short to record changes in the genetic diversity. Given the results presented here and recent evidence of a second population decline, the precise estimation of both gene flow and effective population size via more extensive genetic screening will be critical to effective population management.

Conserving on the edge: genetic variation and structure in northern populations of the endangered plant Dracocephalum ruyschiana L. (Lamiaceae)

Loss of biodiversity is accelerating, including the loss of genetic diversity. Conservation of small, isolated populations may be important, as they can provide valuable contributions to overall genetic variation and long-term viability of species. Furthermore, such populations may play an essential role in adaptation to new environments following changes in e.g. land-use and climate. Dracocephalum ruyschiana is a threatened plant species throughout its European distribution, but 25% of the European populations are situated within Norway. Therefore, the species has its own action plan in Norway, which includes demographic monitoring. However, this monitoring does not cover genetic variation nor is the selection of monitored populations based on genetic differentiation, therefore this fundamental level of biodiversity is overlooked. We analyzed 43 sites using 96 SNPs developed for D. ruyschiana, to investigate whether the monitored populations cover the genetic variation and differentiation found within the Norwegian distribution. The results show structuring and differentiation between populations and indicate that there are at least four distinct genetic groups, of which only two are covered extensively by current demographic monitoring. We suggest that two sites representing the two other genetic groups should be included in the national monitoring program to better conserve the genetic variation found in the Norwegian population of D. ruyschiana. Overall, our results highlight the importance of an integrated, interdisciplinary framework to better monitor and conserve biodiversity at several levels.

Cryptic lineages in the Wolf Cardinalfish living in sympatry on remote coral atolls

Coral reef health and biodiversity is under threat worldwide due to rapid climate change. However, much of the inter- and intra-specific diversity of coral reefs are undescribed even in well studied taxa such as fish. Delimiting previously unrecognised diversity is important for understanding the processes that generate and sustain biodiversity in coral reef ecosystems and informing strategies for their conservation and management. Many taxa that inhabit geographically isolated coral reefs rely on self-recruitment for population persistence, providing the opportunity for the evolution of unique genetic lineages through divergent selection and reproductive isolation. Many such lineages in corals and fish are morphologically similar or indistinguishable. Here, we report the discovery and characterisation of cryptic lineages of the Wolf Cardinalfish, Cheilodipterus artus, from the coral atolls of northwest Australia using multiple molecular markers from mitochondrial (CO1 and D-loop) and nuclear (microsatellites) DNA. Concordant results from all markers identified two highly divergent lineages that are morphologically cryptic and reproductively isolated. These lineages co-occurred at daytime resting sites, but the relative abundance of each lineage was strongly correlated with wave exposure. It appears, therefore, that fish from each lineage are better adapted to different microhabitats. Such cryptic and ecologically based diversity appears to be common in these atolls and may well aid resilience of these systems. Our results also highlight that underwater surveys based on visual identification clearly underestimate biodiversity, and that a taxonomic revision of the Cheilodipterus genus is necessary.

Facets of phylodiversity: evolutionary diversification, divergence and survival as conservation targets

Biodiversity is often described as having multiple facets, including species richness, functional diversity and phylogenetic diversity. In this paper, we argue that phylogenetic diversity itself has three distinct facets-lineage diversification, character divergence and survival time-that can be quantified using distinct branch length metrics on an evolutionary tree. Each dimension is related to different processes of macroevolution, has different spatial patterns and is tied to distinct goals for conserving biodiversity and protecting its future resilience and evolutionary potential. We compared the landscapes identified as top conservation priorities by each of these three metrics in a conservation gap analysis for California, a world biodiversity hotspot, using herbarium data on the biogeography and evolutionary relationships of more than 5000 native plant species. Our analysis incorporated a novel continuous metric of current land protection status, fine-scale data on landscape intactness and an optimization algorithm used to identify complementary priority sites containing concentrations of taxa that are evolutionarily unique, vulnerable due to small range size and/or poorly protected across their ranges. Top conservation priorities included pockets of coastal and northern California that ranked highly for all three phylodiversity dimensions and for species richness, as well as sites uniquely identified by each metric whose value may depend on whether properties such as genetic divergence, high net diversification or independent survival experience are most desirable in an Anthropocene flora.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.

Narrow endemics on coastal plains: Miocene divergence of the critically endangered genus Avellara (Compositae)

Critically endangered species representing ancient, evolutionarily isolated lineages must be given priority when allocating resources for conservation projects. Sound phylogenetic analyses and divergence time estimations are required to detect them, and studies on their population genetics, ecological requirements and breeding system are needed to understand their evolutionary history and to design efficient conservation strategies. Here we present the paradigmatic case of Avellara, a critically endangered monotypic genus of Compositae inhabiting a few swamps in the west-southwest Iberian coastal plains. Our phylogenetic and dating analyses based on nuclear (ITS) and plastid (matK) DNA sequences support a Miocene (>8.6 Ma) divergence between Avellara and closely related genera, resulting in marked morphological and ecological differentiation. We found alarmingly low levels of genetic diversity, based on AFLPs and plastid DNA sequences, and confirmed the prevalence of clonal reproduction. Species distribution modelling suggested a large macroclimatically suitable area for Avellara in the western Iberian Peninsula, but its apparently narrow microecological requirements restrict its distribution to peatlands with low-mineralised waters. Although five populations have been recorded from Spain and Portugal in the past, its current distribution may be reduced to only one population, recurrently found in the last decade but threatened by herbivory and habitat degradation. All this confirms the consideration of Avellara as a threatened species with high phylogenetic singularity, and makes it a flagship species for plant conservation in both Spain and Portugal that should be given priority in the design of in situ and ex situ conservation programmes.

Fuzzy boundaries: color and gene flow patterns among parapatric lineages of the western shovel-nosed snake and taxonomic implication

Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi) that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process.

Genetic population structure in the Antarctic benthos: insights from the widespread amphipod, Orchomenella franklini

Currently there is very limited understanding of genetic population structure in the Antarctic benthos. We conducted one of the first studies of microsatellite variation in an Antarctic benthic invertebrate, using the ubiquitous amphipod Orchomenella franklini (Walker, 1903). Seven microsatellite loci were used to assess genetic structure on three spatial scales: sites (100 s of metres), locations (1-10 kilometres) and regions (1000 s of kilometres) sampled in East Antarctica at Casey and Davis stations. Considerable genetic diversity was revealed, which varied between the two regions and also between polluted and unpolluted sites. Genetic differentiation among all populations was highly significant (F(ST) = 0.086, R(ST) = 0.139, p<0.001) consistent with the brooding mode of development in O. franklini. Hierarchical AMOVA revealed that the majority of the genetic subdivision occurred across the largest geographical scale, with N(e)m≈1 suggesting insufficient gene flow to prevent independent evolution of the two regions, i.e., Casey and Davis are effectively isolated. Isolation by distance was detected at smaller scales and indicates that gene flow in O. franklini occurs primarily through stepping-stone dispersal. Three of the microsatellite loci showed signs of selection, providing evidence that localised adaptation may occur within the Antarctic benthos. These results provide insights into processes of speciation in Antarctic brooders, and will help inform the design of spatial management initiatives recently endorsed for the Antarctic benthos.

Vertebral evolution and the diversification of squamate reptiles

Taxonomic, morphological, and functional diversity are often discordant and independent components of diversity. A fundamental and largely unanswered question in evolutionary biology is why some clades diversify primarily in some of these components and not others. Dramatic variation in trunk vertebral numbers (14 to >300) among squamate reptiles coincides with different body shapes, and snake-like body shapes have evolved numerous times. However, whether increased evolutionary rates or numbers of vertebrae underlie body shape and taxonomic diversification is unknown. Using a supertree of squamates including 1375 species, and corresponding vertebral and body shape data, we show that increased rates of evolution in vertebral numbers have coincided with increased rates and disparity in body shape evolution, but not changes in rates of taxonomic diversification. We also show that the evolution of many vertebrae has not spurred or inhibited body shape or taxonomic diversification, suggesting that increased vertebral number is not a key innovation. Our findings demonstrate that lineage attributes such as the relaxation of constraints on vertebral number can facilitate the evolution of novel body shapes, but that different factors are responsible for body shape and taxonomic diversification.

Connectivity among populations of pygmy whitefish (Prosopium coulterii) in northwestern North America inferred from microsatellite DNA analyses

We studied microsatellite DNA variation in 15 populations of northwestern North American pygmy whitefish ( Prosopium coulterii (Eigenmann and Eigenmann, 1892)), an enigmatic freshwater fish thought to be highly fragmented by residency in deep, cold postglacial lakes. Population subdivision (θ) across 10 loci was 0.12 (P < 0.001) across samples, but one western Alaskan population was more divergent than all others (θ = 0.31–0.41, P < 0.001). Within the Williston Reservoir watershed (WRW), θ averaged 0.08 (P < 0.001) and was positively associated with both the geographic distance between localities (r2 = 0.36, P < 0.001) and the number of branch points interconnecting them (r2 = 0.33, P < 0.001). Differentiation among populations was modeled as the sum of the genetic distances for the stream sections interconnecting them (r2 = 0.74). Differences among subwatersheds with the WRW accounted for 5.1% of the total variation in allele frequencies (P < 0.001). Assignment tests suggested limited movement among lakes, with most inferred dispersal between adjacent watersheds. Coalescent analysis strongly supported a gene flow–drift equilibrium model of population structure over a drift-only model. Effective management of diversity in pygmy whitefish requires the maintenance of stream networks that interconnect lakes within a watershed.

Regional management units for marine turtles: a novel framework for prioritizing conservation and research across multiple scales

Background

Resolving threats to widely distributed marine megafauna requires definition of the geographic distributions of both the threats as well as the population unit(s) of interest. In turn, because individual threats can operate on varying spatial scales, their impacts can affect different segments of a population of the same species. Therefore, integration of multiple tools and techniques — including site-based monitoring, genetic analyses, mark-recapture studies and telemetry — can facilitate robust definitions of population segments at multiple biological and spatial scales to address different management and research challenges.

Methodology/Principal Findings

To address these issues for marine turtles, we collated all available studies on marine turtle biogeography, including nesting sites, population abundances and trends, population genetics, and satellite telemetry. We georeferenced this information to generate separate layers for nesting sites, genetic stocks, and core distributions of population segments of all marine turtle species. We then spatially integrated this information from fine- to coarse-spatial scales to develop nested envelope models, or Regional Management Units (RMUs), for marine turtles globally.

Conclusions/Significance

The RMU framework is a solution to the challenge of how to organize marine turtles into units of protection above the level of nesting populations, but below the level of species, within regional entities that might be on independent evolutionary trajectories. Among many potential applications, RMUs provide a framework for identifying data gaps, assessing high diversity areas for multiple species and genetic stocks, and evaluating conservation status of marine turtles. Furthermore, RMUs allow for identification of geographic barriers to gene flow, and can provide valuable guidance to marine spatial planning initiatives that integrate spatial distributions of protected species and human activities. In addition, the RMU framework — including maps and supporting metadata — will be an iterative, user-driven tool made publicly available in an online application for comments, improvements, download and analysis.

Evolutionary distinctiveness, threat status, and ecological oddity in primates

The EDGE (evolutionarily distinct and globally endangered) conservation program (http://www.edgeofexistence.org) uses a composite measure of threat and phylogenetic isolation to rank species for conservation attention. Using primates as a test case, we examined how species that rank highly with this metric represent the collective from which they are drawn. We considered the ecological and morphological traits, including body mass, diet, terrestriality, and home range size, of all 233 species of primates. Overall, EDGE score and the level of deviance from the mean of 20 different ecological, reproductive, and morphological variables were correlated (mean correlation r =0.14, combined p =1.7 x 10(-14)). Although primates with a high EDGE score had characteristics that made them seem odd, they did not seem to express more ancestral characteristics than expected. Sets of primate species with high EDGE scores will, therefore, collectively capture a broader than expected range of the biology of the clade. If similar patterns hold in other groups, the EDGE metric may be useful for prioritizing biodiversity for conservation.

Conservation prioritization in widespread species: the use of genetic and morphological data to assess population distinctiveness in rainbow trout (Oncorhynchus mykiss) from British Columbia, Canada

Prioritization of efforts to maintain biodiversity is an important component of conservation, but is more often applied to ecosystems or species than within species. We assessed distinctiveness among 27 populations of rainbow trout (Salmonidae: Oncorhynchus mykiss) from British Columbia, Canada, using microsatellite DNA variation (representing historical or contemporary demography) and morphology (representing adaptive variation). Standardized genetic scores, that is, the average deviation across individuals within populations from the overall genetic score generated by factorial correspondence analysis, ranged from 1.05 to 4.90 among populations. Similar standardized morphological scores, generated by principal components analysis, ranged from 1.19 to 5.35. There was little correlation between genetic and morphological distinctiveness across populations, although one population was genetically and morphologically the most distinctive. There was, however, a significant correlation (r = 0.26, P = 0.008) between microsatellite (F_ST) and morphological (P_ST) divergence. We combined measures of allelic richness, genetic variation within, and divergence among, populations and morphological variation to provide a conservation ranking of populations. Our approach can be combined with other measures of biodiversity value (habitat, rarity, human uses, threat status) to rationalize the prioritization of populations, especially for widespread species where geographic isolation across distinct environments promotes intraspecific variability.

How well can captive breeding programs conserve biodiversity? A review of salmonids

Captive breeding programs are increasingly being initiated to prevent the imminent extinction of endangered species and/or populations. But how well can they conserve genetic diversity and fitness, or re-establish self-sustaining populations in the wild? A review of these complex questions and related issues in salmonid fishes reveals several insights and uncertainties. Most programs can maintain genetic diversity within populations over several generations, but available research suggests the loss of fitness in captivity can be rapid, its magnitude probably increasing with the duration in captivity. Over the long-term, there is likely tremendous variation between (i) programs in their capacity to maintain genetic diversity and fitness, and (ii) species or even intraspecific life-history types in both the severity and manner of fitness-costs accrued. Encouragingly, many new theoretical and methodological approaches now exist for current and future programs to potentially reduce these effects. Nevertheless, an unavoidable trade-off exists between conserving genetic diversity and fitness in certain instances, such as when captive-bred individuals are temporarily released into the wild. Owing to several confounding factors, there is also currently little evidence that captive-bred lines of salmonids can or cannot be reintroduced as self-sustaining populations. Most notably, the root causes of salmonid declines have not been mitigated where captive breeding programs exist. Little research has also addressed under what conditions an increase in population abundance due to captive-rearing might offset fitness reductions induced in captivity. Finally, more empirical investigation is needed to evaluate the genetic/fitness benefits and risks associated with (i) maintaining captive broodstocks as either single or multiple populations within one or more facilities, (ii) utilizing cryopreservation or surrogate broodstock technologies, and (iii) adopting other alternatives to captive-rearing such as translocations to new habitats. Management recommendations surrounding these issues are proposed, with the aim of facilitating meta-analyses and more general principles or guidelines for captive-breeding. These include the need for the following: (i) captive monitoring to involve, a priori, greater application of hypothesis testing through the use of well-designed experiments and (ii) improved documentation of procedures adopted by specific programs for reducing the loss of genetic diversity and fitness.

Genetic and phenotypic variation among geographically isolated populations of the globally threatened Dupont’s lark Chersophilus duponti

Identifying genetically and phenotypically distinct populations of threatened species is critical if we are to delineate appropriate plans for their conservation. We conducted an integrated analysis of population genetic structure, historical demographic events, current gene flow (all based on mtDNA sequences) and morphological variation of three geographically separated groups of populations of Dupont's lark Chersophilus duponti, located in the Iberian Peninsula (three populations), Morocco (two populations), and Tunisia (one population). Unusually, this lark species is the only one among the genus Chersophilus. Our results revealed the early historical divergence of an eastern Dupont's lark lineage (in Tunisia) and a western lineage (in Morocco and Spain), consistent with subspecies taxonomy and distribution. The western lineage subsequently split into two lineages, following the isolation of Iberian and African populations. Such pattern of historical differentiation caused great population genetic structure, with differences among geographic areas explaining more than 80% of total genetic variation. Mismatch distributions and coalescent estimates of divergence time showed that lineage divergence was associated with sudden population expansion events, which apparently took place during the last glaciation, when steppe habitats were widespread across the Mediterranean region. Extant populations from different geographic areas hardly shared any haplotype (only one out of 16 ND2 haplotypes was shared by Tunisian and Moroccan Dupont's larks), and consequently gene flow between geographic areas was found to be virtually absent. Apart from showing great genetic differentiation, Dupont's larks from different geographic areas were morphologically distinct, showing substantial variation in body size and feeding-related traits (length of feet and bill). We conclude that Dupont's lark populations isolated in the Iberian Peninsula, Morocco, and Tunisia are distinct evolutionary entities and should be considered as such in conservation plans. Such circumstance sets a daunting conservation challenge that exemplifies the need of incorporating knowledge of historical processes to our general understanding of the demography of threatened species.

Tests of phenotypic and genetic concordance and their application to the conservation of Panamanian golden frogs (Anura, Bufonidae)

Evolutionarily significant units (ESUs) differ in the extent to which they capture, or even consider, adaptive variation, and most such designations are based solely on neutral genetic differences that may not capture variation relevant to species' adaptabilities to changing environmental conditions. While concordant patterns of divergence among data sets (i.e. neutral and potentially non-neutral characters) can strengthen ESU designations, determining whether such criteria are met for highly variable taxa is especially challenging. This study tests whether previously defined ESUs for endangered Panamanian golden frogs (Atelopus varius and Atelopus zeteki) exhibit concordant variation among multiple phenotypic traits and mitochondrial DNA sequences, and the extent to which such divergence corresponds to environmental differences. Multivariate analyses identify phenotypic and genetic differentiation consistent with proposed ESUs and support the status of A. varius and A. zeteki as separate species. Moreover, the significant association detected between ESU co-membership and genetic similarity, which remained strong after removing the effect of geographic distance, also indicates that genetic differences are not simply due to isolation by distance. Two phenotypic characters (body size and the extent of dorsal black patterning) that differ among ESUs also co-vary with environmental differences, suggesting that to the extent that these phenotypic differences are heritable, variation may be associated with adaptive divergence. Lastly, discriminant function analyses show that the frogs can be correctly assigned to ESUs based on simultaneous analysis of multiple characters. The study confirms the merit of conserving the previously proposed golden frog ESUs as well as demonstrates the utility and feasibility of combined analyses of ecological, morphological and genetic variation in evaluating ESUs, especially for highly variable taxa.

Population adaptive index: a new method to help measure intraspecific genetic diversity and prioritize populations for conservation

In conservation biology genetic diversity is recognized as an important criterion to consider when prioritizing populations for protection. Today, population genomics offers the opportunity to evaluate both neutral and adaptive components of genetic diversity directly at the genome level with molecular tools. By screening the genome with many genetic markers, it is possible to detect loci supposedly under natural selection and thus of adaptive significance. We devised a new diversity index, the population adaptive index (PAI), which accounts for the adaptive value of the population it refers to. To estimate this index, we performed a genome scan with amplified fragment length polymorphism markers to identify neutral and selected loci in several populations of a widespread amphibian (common frog, Rana temporaria) and a threatened plant (Austrian dragonhead, Dracocephalum austriacum L.). We then investigated four different conservation strategies aimed at protecting the maximum amount of genetic diversity (neutral or selected). In particular we explored the relevance of the principle of complementarity, usually applied to the protection of species, in the management of intraspecific diversity. This principle advocates the conservation of sets of units that together maximize the species' or genetic diversity, which is in opposition to the traditional approach of targeting populations that are the most diverse individually. Four major conclusions emerged from these results. First, the PAI seemed to be a valuable index to evaluate the adaptive diversities within populations. Second, in the two species, the neutral and adaptive diversities within and among populations were not correlated, so conservation strategies based on the neutral and adaptive indexes would not select the same populations for protection. Third, because of its efficiency in conserving genetic diversity, the principle of complementarity deserves to be used more often for this purpose. Fourth, when neutral and adaptive results conflict, additional arguments (e.g., demography, ecology, and geographic proximity) should be considered together with levels of genetic diversity to determine a conservation strategy.

Conservation genetics of an endemic and endangered epiphytic Laelia speciosa (Orchidaceae)

We used isozymes (16 loci in 11 enzymatic systems) from Laelia speciosa, an endemic and endangered epiphytic orchid of Mexico, to assess the genetic diversity and population genetic structure in nine populations distributed along its geographic range, as well as to detect those populations that are genetically unique and therefore deserve high-priority protection. On average, the genetic diversity was high (percentage of polymorphic loci, P(p) = 76%, mean number of alleles per locus, A = 3.34, the average observed heterozygosity H(O) = 0.302, the average expected heterozygosity H(E) = 0.382). Moderate levels of inbreeding ( f = 0.216, 95% confidence interval = 0.029-0.381) were found. Low levels of genetic differentiation were observed among populations ((p) = 0.040); however, there was a significant correlation between geographic and genetic distances among the populations (Mantel test: r(2) = 0.43, P < 0.05). Populations located within the same mountain range were genetically more similar. Private alleles were found, so proper management requires protection and maintenance of genetic diversity throughout its range. In case of reintroduction, we suggest using individuals propagated from seeds from as many capsules as possible, from close populations. An ex situ conservation strategy also is proposed.

Rangewide molecular structuring in the Utah sucker (Catostomus ardens)

The Utah sucker (Catostomus ardens) is endemic to the Bonneville Basin and the upper Snake River drainage in western North America, and is thought to hybridize with the federally endangered June sucker (Chasmistes liorus mictus) in Utah Lake (Bonneville Basin). Here we describe the discovery of a major subdivision in Utah suckers (4.5% mitochondrial sequence divergence) between the ancient Snake River drainage and the Bonneville Basin. This boundary has not previously been recognized in Utah suckers based on morphologic variation, but has been recently described in two endemic cyprinids in the region. Populations in valleys east of the Wasatch Mountains in Utah clustered with the Snake River populations, suggesting that these valleys may have had an ancient hydrologic connection to the Snake River. We also found evidence of population isolation within the Bonneville Basin, corresponding to two Pleistocene sub-basins of the ancient Lake Bonneville. In contrast, we found no molecular evidence for deep divergence between Utah suckers and June suckers in Utah Lake or for a history of hybridization between divergent lineages in that population, although we recognize that demographic events may have obscured this signal. These findings suggest that the morphological differences between Utah and June suckers in Utah Lake may be the result of strong, and relatively recent, ecological selection. In summary, morphological and molecular characters seem to vary along different axes in different portions of the range of this taxon, providing an interesting system for studying the contributions of neutral and adaptive variation to species diversity.

Phylogeographic Lineages and Species Comparisons in Conservation Analyses: A Case Study of California Herpetofauna

Many phylogeographic studies have revealed strongly diverged lineages within species that are masked by a lack of congruent morphological differentiation. To assess the extent to which the genetic component of diversity affects conservation assessments, we compared spatial patterns of endemism and conservation value for 22 species of Californian amphibians and reptiles with the 75 phylogeographic lineages that they contain. We used bioclimatic distribution modeling with environmental layers to generate 5-km spatial-resolution maps of predicted distribution for each species and lineage. We found concentrations of lineage breaks across the Central Valley, San Francisco Bay, the Sierra Nevada, and the Tehachapi and Trinity ranges. Subdivision of the ranges of species into phylogeographic units revealed novel areas of endemism. Several areas of very high conservation value for lineages were not evident in the species-level analysis. These observations illustrate the importance of considering multiple levels of biodiversity in conservation assessments.

Speciation in reverse: morphological and genetic evidence of the collapse of a three-spined stickleback (Gasterosteus aculeatus) species pair

Historically, six small lakes in southwestern British Columbia each contained a sympatric species pair of three-spined sticklebacks (Gasterosteus aculeatus). These pairs consisted of a 'benthic' and 'limnetic' species that had arisen postglacially and, in four of the lakes, independently. Sympatric sticklebacks are considered biological species because they are morphologically, ecologically and genetically distinct and because they are strongly reproductively isolated from one another. The restricted range of the species pairs places them at risk of extinction, and one of the pairs has gone extinct after the introduction of an exotic catfish. In another lake, Enos Lake, southeastern Vancouver Island, an earlier report suggested that its species pair is at risk from elevated levels of hybridization. We conducted a detailed morphological analysis, as well as genetic analysis of variation at five microsatellite loci for samples spanning a time frame of 1977 to 2002 to test the hypothesis that the pair in Enos Lake is collapsing into a hybrid swarm. Our morphological analysis showed a clear breakdown between benthics and limnetics. Bayesian model-based clustering indicated that two morphological clusters were evident in 1977 and 1988, which were replaced by 1997 by a single highly variable cluster. The most recent 2000 and 2002 samples confirm the breakdown. Microsatellite analysis corroborated the morphological results. Bayesian analyses of population structure in a sample collected in 1994 indicated two genetically distinct populations in Enos Lake, but only a single genetic population was evident in 1997, 2000, and 2002. In addition, genetic analyses of samples collected in 1997, 2000, and 2002 showed strong signals of 'hybrids'; they were genetically intermediate to parental genotypes. Our results support the idea that the Enos Lake species pair is collapsing into a hybrid swarm. Although the precise mechanism(s) responsible for elevated hybridization in the lake is unknown, the demise of the Enos Lake species pair follows the appearance of an exotic crayfish, Pascifasticus lenisculus, in the early 1990s.

Phylogeography of olive ridley turtles (Lepidochelys olivacea) on the east coast of India: implications for conservation theory

Orissa, on the east coast of India, is one of the three mass nesting sites in the world for olive ridley turtles (Lepidochelys olivacea). This population is currently under threat as a result of fishery-related mortality; more than 100 000 olive ridleys have been counted dead in the last 10 years in Orissa. In general, the globally distributed olive ridley turtle has received significantly less conservation attention than its congener, the Kemp's ridley turtle (L. kempi), because the latter is recognized as a distinct species consisting of a single endangered population. Our study of mitochondrial DNA haplotypes suggests that the ridley population on the east coast of India is panmictic, but distinct from all other populations including Sri Lanka. About 96% of the Indian population consisted of a distinct 'K' clade with haplotypes not found in any other population. Nested clade analysis and conventional analysis both supported range expansions and/or long-distance colonization from the Indian Ocean clades to other oceanic basins, which suggested that these are the ancestral source for contemporary global populations of olive ridley turtles. These data support the distinctiveness of the Indian Ocean ridleys, suggesting that conservation prioritization should be based on appropriate data and not solely on species designations.

Population structure of loggerhead shrikes in the California Channel Islands

The loggerhead shrike (Lanius ludovicianus), a songbird that hunts like a small raptor, maintains breeding populations on seven of the eight California Channel Islands. One of the two subspecies, L. l. anthonyi, was described as having breeding populations on six of the islands while a second subspecies, L. l. mearnsi, was described as being endemic to San Clemente Island. Previous genetic studies have demonstrated that the San Clemente Island loggerhead shrike is well differentiated genetically from both L. l. anthonyi and mainland populations, despite the fact that birds from outside the population are regular visitors to the island. Those studies, however, did not include a comparison between San Clemente Island shrikes and the breeding population on Santa Catalina Island, the closest island to San Clemente. Here we use mitochondrial control region sequences and nuclear microsatellites to investigate the population structure of loggerhead shrikes in the Channel Islands. We confirm the genetic distinctiveness of the San Clemente Island loggerhead shrike and, using Bayesian clustering analysis, demonstrate the presence and infer the source of the nonbreeding visitors. Our results indicate that Channel Island loggerhead shrikes comprise three distinct genetic clusters that inhabit: (i) San Clemente Island, (ii) Santa Catalina Island and (iii) the Northern Channel Islands and nearby mainland; they do not support a recent suggestion that all Channel Island loggerhead shrikes should be managed as a single entity.

Molecular biodiversity. Case study: Porifera (sponges)

Biological diversity--or biodiversity--is the term given to the variety of life on Earth and the natural patterns it forms. The biodiversity we see today is the fruit of billions of years of evolution, shaped by natural processes and, increasingly, by the influence of humans. It forms the web of life of which we are an integral part and upon which we so fully depend. The research on molecular biodiversity tries to lay the scientific foundation of a rational conservation policy that has its roots in various disciplines including systematics/taxonomy (species richness), present day ecology (diversity of ecological systems), and functional genetics (genetic diversity). The results of ongoing genome analyses (genome projects and expressed sequence tag projects) and the achievements of molecular evolution may allow us not only to quantitate the diversity of the present biota but also to extrapolate to their diversification in the future. A link between biodiversity and genomics/molecular evolution will create a platform which we hope may facilitate a sustainable management of organismic life and ensure its exploitation for human benefit. In the present review we outline possible strategies, using the Porifera (sponges) as a prominent example. On the basis of solid taxonomy and ecological data, the high value of this phylum for human application becomes obvious, especially with regard to the field of chemical ecology and the desire to find novel potential drugs for clinical use. In addition, the benefit of trying to make sense of molecular biodiversity using sponges as an example can be seen in the fact that the study of these animals, which are "living fossils", gives us a good insight into the history of our planet, especially with respect to the evolution of Metazoa.

The Pacific Salmon Wars: What Science Brings to the Challenge of Recovering Species

▪ Abstract  Politicians, scientists, government agencies, and the public are all engaged in recovery planning for Pacific salmon. In order for science to fulfill its potential in the arena of salmon recovery planning, several shortcomings of the science and its application to decision-making must be rectified. The definition of conservation units using genetic and phylogenetic inference needs to be sharpened. Ecological analyses must get beyond casting blame for past declines in salmon numbers and examine mixed strategies of management that consider interactions between hatcheries, harvest, hydropower, and habitat factors as well as background natural stresses and invasive species. Glib acceptance of expert opinion and extrapolated or inferred data should be tempered. To deal with uncertainty, recovery teams should engage in scenario analyses in which a wide variety of assumptions are played out. Finally, there is a pressing need for analyses aimed at determining what circumstances and communication strategies give science an effective voice in decision-making.

Phylogeography and conservation genetics of the Columbia spotted frog (Rana luteiventris; Amphibia, Ranidae)

The Columbia spotted frog (Rana luteiventris) has a widespread distribution in western Canada and the western US, although the southern reach of its range is highly fragmented into several isolated populations. Threats from various factors have raised concerns regarding the long-term survival of many small, isolated populations. Here, we report a study designed to determine the phylogeographic and conservation genetic parameters of R. luteiventris in the western US. Mitochondrial DNA (mtDNA) sequences were examined for phylogeographic structuring using phylogenetic reconstruction methods, coupled with networking and nested clade analyses. These methods permitted a distinction to be made between historic and demographic forces acting to generate geographical patterning of genetic variation. Phylogenetic analysis revealed four geographically correlated monophyletic clades. Three of these clades correspond to well-defined, nonoverlapping geographical locations in the fragmented portion of the range. The other is comprised of all samples collected from the contiguous range and includes one isolate from northern Wyoming. Networking and nested clade analyses confirmed these results and revealed that historical processes, such as range expansion and vicariance, rather than recurrent gene flow are likely responsible for observed patterns of genetic variation. A measure of genetic variation (theta = 4N(e)mu) revealed that R. luteiventris populations in Utah have a relatively low amount of genetic variation compared with populations in the continuous portion of the range.

Mitochondrial DNA variation in rainbow trout (Oncorhynchus mykiss) across its native range: testing biogeographical hypotheses and their relevance to conservation

North-western North America has been repeatedly glaciated over most of the past two million years, with the most recent glaciation occurring between 60 000 and 10 000 years ago. Intraspecific genetic variation in many species has been shaped by where they survived glaciation and what postglacial recolonization routes were used. In this study, molecular techniques were used to investigate biogeographical, taxonomic and conservation issues in rainbow trout, Oncorhynchus mykiss. Mitochondrial DNA (mtDNA) variation was assessed using a restriction fragment length polymorphism (RFLP) analysis, focusing mainly on the previously understudied northern extent of the species' range. Two phylogenetically distinct mitochondrial lineages were found that differed from each other by up to 1.8% in sequence. Although the geographical distributions of the two clades overlap extensively, diversity and distributional analyses strongly suggest that trout survived glaciation in both coastal and inland refugia followed by postglacial gene flow and secondary contact. Postglacial dispersal into British Columbia most likely occurred from the Queen Charlotte Islands and the Columbia River. Although trout most likely also survived glaciation along the coast of Washington, Oregon and California, as well as near the Bering Strait, evidence suggests that dispersal into British Columbia from these areas was limited. Sequence analysis of mitochondrial haplotypes revealed higher diversity in California than in the northern part of the species' range, indicating an ancient presence of the species in the south. Phylogeographic divergence probably predates adaptive variation in the species as suggested by evidence for parallel evolution of life history types across the range of O. mykiss.