Molecular genetics and the management and conservation of marine organisms

Biochemical and molecular species identification techniques have a broad range of applications in the management and conservation of marine organisms. While species boundaries are not always clearly defined, phylogeneticists utilise autapomorphic characters to distinguish phylogenetic species. Genetic markers discriminate between marine taxa when traditional morphological distinctions are unclear. The applications of these techniques can be divided into four general categories. Firstly, compliance enforcement, which often depends on genetic identification techniques to enable officials to identify the species to which regulations pertain. Secondly, quality control applications, to allow for the testing of marine products to guard against fraudulent substitution with less valuable species, which is particularly pertinent since processing often obliterates identifiable features. Thirdly, a variety of applications to ecological and life-history studies and conservation management are reported. Here, the genetic identification techniques of species from cryptic life-cycle stages or of morphologically indistinct species are an indispensable tool for marine scientists, conservators and managers. Lastly, the application of genetic techniques for sourcing population origin is briefly discussed. The biochemical and molecular techniques applied to species identification all exploit phenotypic or genotypic polymorphisms that are sampled using either tertiary level protein based methods or primary level DNA based methods. In this review, examples of the applications along with the total protein, allozyme, serological, PCR and other DNA based methodologies are briefly described and some generalities with regard to their use are presented.     

Speciation genetics of biological invasions with hybridization

The negative effects of human‐induced habitat disturbance and modification on multiple dimensions of biological diversity are well chronicled ( Turner 1996 ; Harding et al. 1998 ; Lawton et al. 1998 ; Sakai et al. 2001 ). Among the more insidious consequences is secondary contact between formerly allopatric taxa ( Anderson & Hubricht 1938 ; Perry et al. 2002 ; Seehausen 2006 ). How the secondary contact will play out is unpredictable ( Ellstrand et al. 2010 ), but if the taxa are not fully reproductively isolated, hybridization is likely, and if the resulting progeny are fertile, the eventual outcome is often devastating from a conservation perspective ( Rhymer & Simberloff 1996 ; Wolf et al. 2001 ; McDonald et al. 2008 ). In this issue of Molecular Ecology, Steeves et al. (2010) present an analysis of hybridization between two avian species, one of which is critically endangered and the other of which is invasive. Their discovery that the endangered species has not yet been hybridized to extinction is promising and not what one would necessarily expect from theory.     

Boom‐bust dynamics in biological invasions: towards an improved application of the concept

Boom‐bust dynamics – the rise of a population to outbreak levels, followed by a dramatic decline – have been associated with biological invasions and offered as a reason not to manage troublesome invaders. However, boom‐bust dynamics rarely have been critically defined, analyzed, or interpreted. Here, we define boom‐bust dynamics and provide specific suggestions for improving the application of the boom‐bust concept. Boom‐bust dynamics can arise from many causes, some closely associated with invasions, but others occurring across a wide range of ecological settings, especially when environmental conditions are changing rapidly. As a result, it is difficult to infer cause or predict future trajectories merely by observing the dynamic. We use tests with simulated data to show that a common metric for detecting and describing boom‐bust dynamics, decline from an observed peak to a subsequent trough, tends to severely overestimate the frequency and severity of busts, and should be used cautiously if at all. We review and test other metrics that are better suited to describe boom‐bust dynamics. Understanding the frequency and importance of boom‐bust dynamics requires empirical studies of large, representative, long‐term data sets that use clear definitions of boom‐bust, appropriate analytical methods, and careful interpretations.     

Molecular systematics for taxonomic placement of a gorilla of uncertain origin

An adult male gorilla was donated from private ownership in 1994 to Zoo Atlanta and became part of the American Zoo and Aquarium Association's Gorilla Species Survival Plan. This animal, Ivan, was captured as an infant in Africa in 1964. Ambiguity regarding origin and concomitant sub‐species designation was resolved by analyzing the cytochrome oxidase II mitochondrial gene known to contain eight diagnostic sites for gorilla sub‐species. Ivan has the diagnostic profile that characterizes the western clade Gorilla gorilla gorilla. Zoo Biol 18:429–432, 1999. © 1999 Wiley‐Liss, Inc.     

Dynamic economic analysis on invasive species management: Some policy implications of catchability

The problem of controlling invasive species has emerged as a global issue. In response to invasive species threats, governments often propose eradication. This article challenges the eradication view by studying optimal strategies for controlling invasive species in a simple dynamic model. The analysis mainly focuses on deriving policy implications of catchability in a situation where a series of controlling actions incurs operational costs that derive from the fact that catchability depends on the current stock size of invasive species. We analytically demonstrate that the optimal policy changes drastically, depending on the sensitivity of catchability in response to a change in the stock size, as well as on the initial stock. If the sensitivity of catchability is sufficiently high, the constant escapement policy with some interior target level is optimal. In contrast, if the sensitivity of catchability is sufficiently low, there could exist a threshold of the initial stock which differentiates the optimal action between immediate eradication and giving-up without any control. In the intermediate range, immediate eradication, giving-up without any control, or more complex policies may be optimal. Numerical analysis is employed to present economic intuitions and insights in both analytically tractable and intractable cases.     

Global-scale analyses of chemical ecology and population genetics in the invasive Argentine ant

Ants are some of the most abundant and ecologically successful terrestrial organisms, and invasive ants rank among the most damaging invasive species. The Argentine ant is a particularly well-studied invader, in part because of the extreme social structure of introduced populations, known as unicoloniality. Unicolonial ants form geographically vast supercolonies, within which territorial behaviour and intraspecific aggression are absent. Because the extreme social structure of introduced populations arises from the widespread acceptance of conspecifics, understanding how this colonymate recognition occurs is key to explaining their success as invaders. Here, we present analyses of Argentine ant recognition cues (cuticular hydrocarbons) and population genetic characteristics from 25 sites across four continents and the Hawaiian Islands. By examining both hydrocarbon profiles and microsatellite genotypes in the same individual ants, we show that native and introduced populations differ in several respects. Both individual workers and groups of nestmates in the introduced range possess less diverse chemical profiles than ants in the native range. As previous studies have reported, we also find that introduced populations possess much lower levels of genetic diversity than populations in the native range. Interestingly, the largest supercolonies on several continents are strikingly similar to each other, suggesting that they arose from a shared introduction pathway. This high similarity suggests that these geographically far-flung ants may still recognize and accept each other as colonymates, thus representing distant nodes of a single, widely distributed supercolony. These findings shed light on the behaviour and sociality of these unicolonial invaders, and pose new questions about the history and origins of introduced populations.     

Gene trees and species trees – mutual influences and interdependences of population genetics and systematics

Both population genetics and systematics are core disciplines of evolutionary biology. While systematics deals with genealogical relationships among taxa, population genetics has mainly been based on allele frequencies and the distribution of genetic variants whose genealogical relations could for a long time, due mainly to methodological constraints, not be inferred. The advent of mitochondrial DNA analyses and modern sequencing techniques in the 1970s revolutionized evolutionary genetic studies and gave rise to molecular phylogenetics. In the wake of this new development systematic approaches and principles were incorporated into intraspecific studies at the population level, e.g. the concept of monophyly which is used to delineate evolutionarily significant units in conservation biology. A new discipline combining phylogenetic analyses of genetic lineages with their geographic distribution ('phylogeography') was introduced as an explicit synthesis of population genetics and systematics. On the other hand, it has increasingly become obvious that discordances between gene trees and species trees not only result from spurious data sets or methodological flaws in phylogenetic analyses, but that they often reflect real population genetic processes such as lineage sorting or hybridization. These processes have to be taken into account when evaluating the reliability of gene trees to avoid wrong phylogenetic conclusions. The present review focuses on the phenomenon of non-phylogenetic sorting of ancestral polymorphisms, its probability and its consequences for molecular systematics.     

Towards a better understanding of the higher systematics of Nymphalidae (Lepidoptera: Papilionoidea)

Research on the molecular systematics of higher taxa in the butterfly family Nymphalidae (Lepidoptera) is only just beginning. Outgroup selection is difficult at the moment due to the lack of consensus on the basal relationships of the major groups in Nymphalidae. We identify four major clades in the Nymphalidae based on a cladistic analysis of one mitochondrial gene sequence (COI, 1450 bp) and two nuclear gene sequences (EF-1alpha, 1064 bp, and wingless, 412-415 bp) from 54 exemplar species sampled from all currently recognized subfamilies. The COI data set was found to be highly incongruent with the nuclear data sets and a Partitioned Bremer Support analysis shows that the COI data set largely undermines support for most clades. Transitions at the third codon positions of the COI data set were highly saturated, but analyzing the combined data set with the COI third positions removed did not change the results. The major clades we found are termed the danaine clade (including Danainae), the satyrine clade (including Charaxinae, Satyrinae, Calinaginae, and Morphinae), the heliconiine clade (including Heliconiinae and Limenitidinae excluding Biblidini, Cyrestini, Pseudergolini, and Coeini) and the nymphaline clade (including Nymphalinae, Apaturinae, and Coeini, Cyrestini, Pseudergolini, and Biblidini from Limenitidinae). The heliconiine and nymphaline clades are sister groups, while the most parsimonious explanation for the combined data set places the danaine clade as the most basal large group of Nymphalidae. Our results give one of the strongest hypotheses for the subfamilial relationships within Nymphalidae. We were able to resolve the polyphyletic nature of Limenitidinae, which we recommend to be split into three subfamilies: Limenitidinae, Biblidinae, and Cyrestinae. The tribe Coeini belongs in Nymphalinae.     

Symbiodinium population genetics: testing for species boundaries and analysing samples with mixed genotypes

Population genetic markers are increasingly being used to study the diversity, ecology and evolution of Symbiodinium, a group of eukaryotic microbes that are often mutualistic with reef‐building corals. Population genetic markers can resolve individual clones, or strains, from samples of host tissue; however, samples may comprise different species that may confound interpretations of gene flow and genetic structure. Here, we propose a method for resolving species from population genetic data using tests for genetic recombination. Assigning individuals to genetically recombining populations prior to further analyses avoids critical errors in the interpretation of gene flow and dispersal. To demonstrate the effectiveness of the approach, we first apply this method to a simulated data set. We then use the method to resolve two species of host generalist Symbiodinium that commonly co‐occur in reef‐building corals collected from Indo‐West Pacific reefs. We demonstrate that the method is robust even when some hosts contain genotypes from two distinct species. Finally, we examine population genetic data sets from two recently published papers in Molecular Ecology. We show that each strongly supports a two species interpretation, which significantly changes the original conclusions presented in these studies. When combined with available phylogenetic and ecological evidence, the use of population genetic data offers a robust method for unambiguously delimiting morphologically cryptic species.     

Optimal invasive species management under multiple uncertainties

The management programs for invasive species have been proposed and implemented in many regions of the world. However, practitioners and scientists have not reached a consensus on how to control them yet. One reason is the presence of various uncertainties associated with the management. To give some guidance on this issue, we characterize the optimal strategy by developing a dynamic model of invasive species management under uncertainties. In particular, focusing on (i) growth uncertainty and (ii) measurement uncertainty, we identify how these uncertainties affect optimal strategies and value functions. Our results suggest that a rise in growth uncertainty causes the optimal strategy to involve more restrained removals and the corresponding value function to shift up. Furthermore, we also find that a rise in measurement uncertainty affects optimal policies in a highly complex manner, but their corresponding value functions generally shift down as measurement uncertainty rises. Overall, a rise in growth uncertainty can be beneficial, while a rise in measurement uncertainty brings about an adverse effect, which implies the potential gain of precisely identifying the current stock size of invasive species.     

Molecular genetic approaches to elucidate the ecological and evolutionary issues associated with biological invasions

Biological invasions may cause serious damage to the native environments and threaten the native biodiversity. Molecular genetic approaches have been found to be powerful tools for investigating the ecological and evolutionary aspects of biological invasions because the genetic structure and level of genetic variation of an invasive species are changed following its invasion. The present article reviews the use of molecular markers in addressing various aspects of invasive species. The application of these techniques has shown that many invasive species are actually "cryptic" species – species whose uniqueness is only recognizable at the genetic level. An estimation of the actual number of invasive species is essential when evaluating its ecological and economic impacts. Molecular genetic approaches have also enabled the source populations of invasive species to be identified. Reconstructions of invasion histories are crucial to preventing future invasions and conserving the native biodiversity, while comparisons of genetic variations between the native and introduced populations provide valuable opportunities to elucidate the mechanisms of rapid adaptation demonstrated by many invasive species.     

Comparison of the population genetics and densities of five pinanga palm species at kuala belalong, brunei

This study investigated the effect of population density on the population genetic structure of five co-occurring congeneric understorey palm species: Pinanga aristata, P. sp. aff. brevipes, P. dumetosa, P. tenella var. tenella and P. veitchii, all endemic to northern Borneo. The average population densities of the study species varied across a wide spectrum, ranging from 343 (plants per ha) in P. tenella to 10 (plants per ha) in P. veitchii. All species of Pinanga palms studied had quite high levels of genetic diversity (HE: 0.379, 0.256, 0.294, 0.133, 0.352). Genetic diversity (HE) was correlated with population density (D; rs = - 0.433, P < 0.01) and the average distance to the nearest conspecific neighbour (NN; rs = 0.576, P < 0.001) such that the most-dense species had less genetic diversity and the less-dense species had greater genetic diversity. Gene flow (Nm) among populations approximately followed a gradient of increasing species density and abundance, such that the most common species P. dumestosa had the greatest gene flow (Nm = 2.268) between its populations and the rarest, most sparsely distributed species P. sp. aff. brevipes had the lowest (Nm = 0.698). All species of Pinanga were effectively inbred (F: 0.760, 0.856, 0.640, 0.753, 0.674). The amount of homozygosity and inbreeding (HO, F) were not correlated (P > 0.05) with population density (D) or the distance between nearest neighbouring plants of the same species (NN).     

Molecular approaches for a better understanding of the epidemiology and population genetics of Leishmania

Molecular approaches are being used increasingly for epidemiological studies of visceral and cutaneous leishmaniases. Several molecular markers resolving genetic differences between Leishmania parasites at species and strain levels have been developed to address key epidemiological and population genetic questions. The current gold standard, multilocus enzyme typing (MLEE), needs cultured parasites and lacks discriminatory power. PCR assays identifying species directly with clinical samples have proven useful in numerous field studies. Multilocus sequence typing (MLST) is potentially the most powerful phylogenetic approach and will, most probably, replace MLEE in the future. Multilocus microsatellite typing (MLMT) is able to discriminate below the zymodeme level and seems to be the best candidate for becoming the gold standard for distinction of strains. Population genetic studies by MLMT revealed geographical and hierarchic population structure in L. tropica, L. major and the L. donovani complex. The existence of hybrids and gene flow between Leishmania populations suggests that sexual recombination is more frequent than previously thought. However, typing and analytical tools need to be further improved. Accessible databases should be created and sustained for integrating data obtained by different researchers. This would allow for global analyses and help to avoid biases in analyses due to small sample sizes.     

Intracoastal shipping drives patterns of regional population expansion by an invasive marine invertebrate

Understanding the factors contributing to expansion of nonnative populations is a critical step toward accurate risk assessment and effective management of biological invasions. Nevertheless, few studies have attempted explicitly to test hypotheses regarding factors driving invasive spread by seeking correlations between patterns of vector movement and patterns of genetic connectivity. Herein, we describe such an attempt for the invasive tunicate Styela clava in the northeastern Pacific. We utilized microsatellite data to estimate gene flow between samples collected throughout the known range of S. clava in the region, and assessed correlation of these estimates with patterns of intracoastal commercial vessel traffic. Our results suggest that recent shipping patterns have contributed to the contemporary distribution of genetic variation. However, the analysis also indicates that other factors—including a complex invasion history and the influence of other vectors—have partially obscured genetic patterns associated with intracoastal population expansion.     

Large scale unicoloniality: the population and colony structure of the invasive Argentine ant (<Emphasis Type="Italic">Linepithema humile</Emphasis>) in New Zealand

The Argentine ant is native to South America and has spread widely across the globe. In this study, we use genetic analyses and behavioural assays to examine the colony structure of Argentine ants in New Zealand. Diet modification studies were also carried out in order to help identify what factors influence these behavioural assays. There was no aggression observed between any pairings tested across the North Island of New Zealand, though we found that diet manipulations in the laboratory could lead to low levels of aggression between previously amiable Argentine ant nests. The New Zealand population of Argentine ants was characterized by low levels of genetic variation in six microsatellite loci from their nuclear genome. Additionally, the population also lacked significant genetic structuring with no patterns of regional differentiation or isolation by distance. An analysis of molecular variation(AMOVA) found that themajority of genetic variation was present at a nest level (93% of total genetic variance), with little genetic differentiation observed within or between regions (3 – 4% of total genetic variance). No correlation between aggression and genetic relatedness was observed. This evidence suggests that Argentine ants in New Zealand effectively form a unicolonial population, which is likely the result of colonization from a single source population. As far as we know, this is the first country to have an entirely unicolonial population of Argentine ants. Received 21 February 2007; revised 20 May 2007; accepted 22 May 2007.     

Microsatellite markers for population and conservation genetics of tropical trees

We have developed microsatellite or simple sequence repeat (SSR) genetic markers for the tropical tree Pithecellobium elegans (Mimosoideae). The frequency of this class of marker is estimated and the level and distribution of variability at these markers is assessed and contrasted to that found at isozyme markers in the same populations. The results indicate that SSR loci are powerful tools for the analysis of population structure and that, in these populations, they provide a means of accurately examining two important parameters in conservation biology, gene flow and paternity.     

The role of aggression in range expansion and biological invasions

Traits that aid in the invasion process should exhibit a gradient across the expansion range in response to changing selection pressures. Aggression has been repeatedly associated with invasion success in many taxa, as it may help invaders to wrestle the resources from other species which enhances their success in a novel environment. However, aggression primarily al lows individuals to overcome conspecific rivals, providing advantages in competition over resources. Agonistic prowess could therefore increase fitness at both ends of the expansion gradient. Here we review the role of aggression in range expansion of in vasive species, and its potential role as a driver of range expansion. We analyze how these different mechanisms could affect trait variation in expanding and invasive populations. Specifically, we look at how aggression could help dilate the edges of a popula tion through niche competition, as well as lead to exclusion from the center （Le. areas of high population density） by the conspe cities. Both of these processes will result in a characteristic spatial distribution of phenotypes related to aggression that could provide insights into the ecological pressures and dynamics of expanding populations, potentially providing clues to their success as niche competitors and invasive species     

A mechanistic model for understanding invasions: using the environment as a predictor of population success

Aim We set out to develop a temperature‐ and salinity‐dependent mechanistic population model for copepods that can be used to understand the role of environmental parameters in population growth or decline. Models are an important tool for understanding the dynamics of invasive species; our model can be used to determine an organism’s niche and explore the potential for invasion of a new habitat. Location Strait of Georgia, British Columbia, Canada. Methods We developed a birth rate model to determine the environmental niche for an estuarine copepod. We conducted laboratory experiments to estimate demographic parameters over a range of temperatures and salinities for Eurytemora affinis collected from the Nanaimo Estuary, British Columbia (BC). The parameterized model was then used to explore what environmental conditions resulted in population growth vs. decline. We then re‐parameterized our model using previously published data for E. affinis collected in the Seine Estuary, France (SE), and compared the dynamics of the two populations. Results We established regions in temperature–salinity space where E. affinis populations from BC would likely grow vs. decline. In general, the population from BC exhibited positive and higher intrinsic growth rates at higher temperatures and salinities. The population from SE exhibited positive and higher growth rates with increasing temperature and decreasing salinity. These different relationships with environmental parameters resulted in predictions of complex interactions among temperature, salinity and growth rates if the two subspecies inhabited the same estuary. Main conclusions We developed a new mechanistic model that describes population dynamics in terms of temperature and salinity. This model may prove especially useful in predicting the potential for invasion by copepods transported to Pacific north‐west estuaries via ballast water, or in any system where an ecosystem is subject to invasion by a species that shares demographic characteristics with an established (sub)species.     

Cryptic species, native populations and biological invasions by a eucalypt forest pathogen

Human‐associated introduction of pathogens and consequent invasions is very evident in areas where no related organisms existed before. In areas where related but distinct populations or closely related cryptic species already exist, the invasion process is much harder to unravel. In this study, the population structure of the Eucalyptus leaf pathogen Teratosphaeria nubilosa was studied within its native range in Australia, including both commercial plantations and native forests. A collection of 521 isolates from across its distribution was characterized using eight microsatellite loci, resulting in 112 multilocus haplotypes (MLHs). Multivariate and Bayesian analyses of the population conducted in structure revealed three genetically isolated groups (A, B and C), with no evidence for recombination or hybridization among groups, even when they co‐occur in the same plantation. DNA sequence data of the ITS (n = 32), β‐tubulin (n = 32) and 27 anonymous loci (n = 16) were consistent with microsatellite data in suggesting that T. nubilosa should be considered as a species complex. Patterns of genetic diversity provided evidence of biological invasions by the pathogen within Australia in the states of Western Australia and New South Wales and helped unravel the pattern of invasion beyond Australia into New Zealand, Brazil and Uruguay. No significant genetic differences in pathogen populations collected in native forests and commercial plantations were observed. This emphasizes the importance of sanitation in the acquisition of nursery stock for the establishment of commercial plantations.