"Nested" cryptic diversity in a widespread marine ecosystem engineer: a challenge for detecting biological invasions

<p>Abstract</p> <p>Background</p> <p>Ecosystem engineers facilitate habitat formation and enhance biodiversity, but when they become invasive, they present a critical threat to native communities because they can drastically alter the receiving habitat. Management of such species thus needs to be a priority, but the poorly resolved taxonomy of many ecosystem engineers represents a major obstacle to correctly identifying them as being either native or introduced. We address this dilemma by studying the sea squirt <it>Pyura stolonifera</it>, an important ecosystem engineer that dominates coastal communities particularly in the southern hemisphere. Using DNA sequence data from four independently evolving loci, we aimed to determine levels of cryptic diversity, the invasive or native status of each regional population, and the most appropriate sampling design for identifying the geographic ranges of each evolutionary unit.</p> <p>Results</p> <p>Extensive sampling in Africa, Australasia and South America revealed the existence of "nested" levels of cryptic diversity, in which at least five distinct species can be further subdivided into smaller-scale genetic lineages. The ranges of several evolutionary units are limited by well-documented biogeographic disjunctions. Evidence for both cryptic native diversity and the existence of invasive populations allows us to considerably refine our view of the native versus introduced status of the evolutionary units within <it>Pyura stolonifera </it>in the different coastal communities they dominate.</p> <p>Conclusions</p> <p>This study illustrates the degree of taxonomic complexity that can exist within widespread species for which there is little taxonomic expertise, and it highlights the challenges involved in distinguishing between indigenous and introduced populations. The fact that multiple genetic lineages can be native to a single geographic region indicates that it is imperative to obtain samples from as many different habitat types and biotic zones as possible when attempting to identify the source region of a putative invader. "Nested" cryptic diversity, and the difficulties in correctly identifying invasive species that arise from it, represent a major challenge for managing biodiversity.</p

Three fishes in one : cryptic species in an Amazonian floodplain forest specialist

Accurately describing biodiversity in tropical regions such as Amazonia is difficult because of insufficient morphological inventories and the lack of studies on the distribution of genetic diversity. Aquatic organisms from Amazonian flooded forests are generally expected to move laterally along the forests during the annual inundation cycle, a behaviour that should promote admixture of populations and reduce within-drainage speciation. We used an unprecedented fine-scale sampling effort and multiple DNA markers to quantify region-wide population differentiation in an Amazonian floodplain forest specialist, the black-wing hatchet fish Carnegiella marthae (Myers, 1927). Our study revealed three previously unsuspected and ancient cryptic species of black-wing hatchet fish in the Rio Negro floodplain (RNF), in central Amazonia. Two species produce occasional first-generation hybrids. The third and rarer species, although found in extreme sympatry with another species, appears to be reproductively isolated, and also differs in external morphology and dentition. Our findings have important implications for guiding conservation management because C. marthae is harvested commercially in the RNF ornamental fishery. They also suggest that the diversity of Amazonian ichthyofauna is vastly underestimated, including that found in landscapes lacking contemporary barriers to account for popula tion divergence and speciation.13 page(s

Use of SSCP to improve the efficiency of microsatellite identification from microsatellite-enriched libraries

An inefficient aspect of marker identification from microsatellite-enriched libraries is the proportion of clones with identical sequences. This can substantially increase the number of clones that need to be sequenced in order to identify a sufficient number of microsatellite loci. We propose the use of single-stranded conformation polymorphism (SSCP) analysis to identify unique clones prior to sequencing. We used this approach prior to sequencing from microsatellite-enriched libraries for three marine invertebrate species and were able to obtain a given number of unique clone sequences for only 28% of the sequencing effort that would have been required without SSCP screening.3 page(s

Genetic evidence for different scales of connectivity in a marine mollusc

Recent studies of connectivity in marine populations have suggested that larval retention and local recruitment are more common than previously considered. Here we used genetic data to investigate the scale of connectivity and patterns of recruitment in the abalone Haliotis coccoradiata, a broadcast spawner with a short larval stage. Although we detected weak but significant genetic differentiation (FST) between populations over a scale of approximately 1000 km, the pattern did not fit an isolation-by-distance (IBD) model, suggesting relatively long dispersal distances. However, individual-based multilocus spatial autocorrelation identified fine-scale genetic structure within a range of 20 km, suggesting short distance dispersal and local recruitment. Simple computer simulations in which all dispersal was restricted to within this scale (mean 10 km) suggested that a significant IBD result would most likely be generated under such a dispersal scenario. The lack of a significant IBD suggests infrequent long-distance dispersal is also likely and this is further supported by oceanographic particle dispersal modelling, which shows that larvae could be transported over large distances by ocean currents. Our results suggest that recruitment occurs primarily over a small spatial scale in a species that also has the ability to disperse over considerably greater distances.10 page(s

Microsatellite DNA markers for analysis of population structure in the sea urchin Centrostephanus rodgersii.

We describe the development of 13 variable microsatellites developed to investigate population structure and dispersal in the sea urchin Centrostephanus rodgersii. This species is the dominant grazing herbivore in southeast Australian coastal waters and has the ability to modify benthic community structure. The microsatellites we identified showed a range of allele numbers (4–21) and expected heterozygosity (0.32–0.91) in two sampled populations. Contrary to previous findings in free-spawning marine invertebrates, genotype proportions in neither population deviated significantly from Hardy–Weinberg expectations.3 page(s

Comparison of traditional and environmental DNA survey methods for detecting rare and abundant freshwater fish

Detecting rare species is often a necessity for conservation and management, yet challenging for many field survey methods. Environmental DNA (eDNA) is a highly promising solution that has been shown to outperform many established survey methods. Macquarie perch (Macquaria australasica) is an endangered native species that has declined significantly in range and abundance. Detection of M. australasica was compared with an abundant alien fish species (Oncorhynchus mykiss) using eDNA and three conventional survey methods: gill nets, electrofishing and fyke nets. eDNA occupancy estimates for both fish species were compared using four different models to investigate what effect these differences have on false positives and false negatives for the rare and common fish species. These models used unadjusted eDNA detections in water samples, eDNA detections that have been screened using a limit of detection method to remove potential false positives, eDNA data supplemented with a second survey method, or eDNA data augmented with sequencing of positive polymerase chain reaction replicates. eDNA surveying as a single detection method was found to be more efficient and sensitive compared with each capture method separately and combined. Occupancy estimates for the common and rare species did not vary significantly between the four site occupancy-detection models, suggesting that supplementary data may not have as much effect on occupancy estimates compared with other approaches such as temporal or spatial sampling. We conclude that eDNA outperforms the three established survey methods for both a rare and common freshwater fish species. Although there was no significant effect of augmenting eDNA survey methods with other survey data, additional data may improve confidence in detection, and provide confirmatory evidence for unexpected or new detections of a species.Icon Water funded the fish survey. ACT Parks and Lands facilitated access to survey sites.Fieldwork was conducted in Ngunnawal country under approval ofthe University of Canberra animal ethics committee (Project CEAE16-11)