Hidden Biodiversity Research Articles

Hidden biodiversity in an ancient lake: phylogenetic congruence between Lake Tanganyika tropheine cichlids and their monogenean flatworm parasites.

The stunning diversity of cichlid fishes has greatly enhanced our understanding of speciation and radiation. Little is known about the evolution of cichlid parasites. Parasites are abundant components of biodiversity, whose diversity typically exceeds that of their hosts. In the first comprehensive phylogenetic parasitological analysis of a vertebrate radiation, we study monogenean parasites infecting tropheine cichlids from Lake Tanganyika. Monogeneans are flatworms usually infecting the body surface and gills of fishes. In contrast to many other parasites, they depend only on a single host species to complete their lifecycle. Our spatially comprehensive combined nuclear-mitochondrial DNA dataset of the parasites covering almost all tropheine host species (N = 18), reveals species-rich parasite assemblages and shows consistent host-specificity. Statistical comparisons of host and parasite phylogenies based on distance and topology-based tests demonstrate significant congruence and suggest that host-switching is rare. Molecular rate evaluation indicates that species of Cichlidogyrus probably diverged synchronically with the initial radiation of the tropheines. They further diversified through within-host speciation into an overlooked species radiation. The unique life history and specialisation of certain parasite groups has profound evolutionary consequences. Hence, evolutionary parasitology adds a new dimension to the study of biodiversity hotspots like Lake Tanganyika.

Hidden biodiversity in the Iberian Mesovoid Shallow Substratum (MSS): New and poorly known species of the millipede genus Archipolydesmus Attems, 1898 (Diplopoda, Polydesmidae)

Systematic sampling of the Mesovoid Shallow Substratum (MSS) at several sites in three regions of the Iberian Peninsula has revealed two new and one very poorly known species of the genus ArchipolydesmusAttems, 1898. These are the first records of Archipolydesmus in the MSS, although the genus had previously been recorded from several caves in southern Spain. Archipolydesmus foliatus sp. nov. shows inter-population variability between different mountain massifs of the province of Alicante, as well as intra-population variability at some sites; A. altibaeticus sp. nov. exclusively inhabits the MSS of the highest screes of Sierra Nevada (3000masl) in the province of Granada, and it closely resembles Archipolydesmus maroccanusAttems, 1898; from North Africa; Archipolydesmus bedeli (Brölemann, 1902) had only been re-collected once since its description, and the male, hitherto unknown, is described here. Detailed SEM documentation of the main characters of each species is provided, and a discussion on the implications of these findings in the MSS is provided. Also, a distribution map, an updated key to species of the genus in English, and a brief review of millipedes found in the MSS are provided.

Morphological and molecular characteristics of Homoeostrichus formosana sp. nov. (Dictyotaceae, Phaeophyceae) from Taiwan.

BackgroundIn the marine brown macroalgae, the morphological characters are highly similar between two widely distributed genera, Homoeostrichus and Zonaria (Dictyotaceae), thereby resulting in the difficulty of exploring their hidden biodiversity. Owing to the help of the molecular tools, it is now easy for scientists to objectively describe a new species in nature. In this study, we make a description on the Homoeostrichus formosana sp. nov. from Taiwan, Indo-Pacific Ocean based on the morphological evidence and molecular data.ResultsOur morphological observations revealed that this species has marginal row of apical cells responsible for thallus growth and the thallus with four layers of cells except the marginal regions. The cortical cell lies upon each medullary cell in transverse section, and two cortical cells upon each medullary cell in longitudinal section. Tetrasporangium is developed from cortical cell with stalk cell and singly scattered over the thallus surface, and has no indusia and paraphyses. Molecularly, the phylogenetic trees based on SSU, psaA, psbA, and rbcL gene sequences supported that Homoeostrichus species are closely related to Exallosorus species and clearly separated from each others in addition to Zonaria species.ConclusionsHomoeostrichus formosana sp. nov. can now be clearly distinguished from E. harveyanus and Japanese H. flabellatus.Electronic supplementary materialThe online version of this article (doi:10.1186/1999-3110-54-13) contains supplementary material, which is available to authorized users.

Hidden Biodiversity in an Ecologically Important Freshwater Amphipod: Differences in Genetic Structure between Two Cryptic Species

Cryptic species, i.e. species that are morphologically hard to distinguish, have been detected repeatedly in various taxa and ecosystems. In order to evaluate the importance of this finding, we have to know in how far cryptic species differ in various aspects of their biology. The amphipod Gammarus fossarum is a key invertebrate in freshwater streams and contains several cryptic species. We examined the population genetic structure, genetic diversity and demographic history of two of them (type A and type B) using microsatellite markers and asked whether they show significant differences. We present results of population genetic analyses based on a total of 37 populations from the headwaters of two major European drainages, Rhine and Rhone. We found that, in both species, genetic diversity was geographically structured among and within drainages. For type A in the Rhine and type B in the Rhone, we detected significant patterns of isolation by distance. The increase of genetic differentiation with geographical distance, however, was much higher in type A than in type B. This result indicates substantial interspecific differences in population history and/or the extent of current gene flow between populations. In the Rhine, type B does not show evidence of isolation by distance, and population differentiation is relatively low across hundreds of kilometres. The majority of these populations also show signatures of recent bottlenecks. These patterns are consistent with a recent expansion of type B into the Rhine drainage. In summary, our results suggest considerable and previously unrecognized interspecific differences in the genetic structure of these cryptic keystone species.

DNA barcoding reveals both known and novel taxa in the Albitarsis Group (Anopheles: Nyssorhynchus) of Neotropical malaria vectors

BackgroundMosquitoes belonging to the Albitarsis Group (Anopheles: Nyssorhynchus) are of importance as malaria vectors across the Neotropics. The Group currently comprises six known species, and recent studies have indicated further hidden biodiversity within the Group. DNA barcoding has been proposed as a highly useful tool for species recognition, although its discriminatory utility has not been verified in closely related taxa across a wide geographic distribution.MethodsDNA barcodes (658 bp of the mtDNA Cytochrome c Oxidase - COI) were generated for 565 An. albitarsis s.l. collected in Argentina, Brazil, Colombia, Paraguay, Trinidad and Venezuela over the past twenty years, including specimens from type series and type localities. Here we test the utility of currently advocated barcoding methodologies, including the Kimura-two-parameter distance model (K2P) and Neighbor-joining analysis (NJ), for determining species delineation within mosquitoes of the Neotropical Albitarsis Group of malaria vectors (Anopheles: Nyssorhynchus), and compare results with Bayesian analysis.ResultsSpecies delineation through barcoding analysis and Bayesian phylogenetic analysis, fully concur. Analysis of 565 sequences (302 unique haplotypes) resolved nine NJ tree clusters, with less than 2% intra-node variation. Mean intra-specific variation (K2P) was 0.009 (range 0.002 - 0.014), whereas mean inter-specific divergence were several-fold higher at 0.041 (0.020 - 0.056), supporting the reported "barcoding gap". These results show full support for separate species status of the six known species in the Albitarsis Group (An. albitarsis s.s., An. albitarsis F, An. deaneorum, An. janconnae, An. marajoara and An. oryzalimnetes), and also support species level status for two previously detected lineages - An. albitarsis G &An. albitarsis I (designated herein). In addition, we highlight the presence of a unique mitochondrial lineage close to An. deaneorum and An. marajoara (An. albitarsis H) from Rondônia and Mato Grosso in southwestern Brazil. Further integrated studies are required to confirm the status of this lineage.ConclusionsDNA barcoding provides a reliable means of identifying both known and undiscovered biodiversity within the closely related taxa of the Albitarsis Group. We advocate its usage in future studies to elucidate the vector competence and respective distributions of all eight species in the Albitarsis Group and the novel mitochondrial lineage (An. albitarsis H) recovered in this study.

Hidden biodiversity in rare northern Australian vertebrates: the case of the clawless geckos (Crenadactylus, Diplodactylidae) of the Kimberley

Context The phylogenetic diversity and biogeography of most animal and plant lineages endemic to the Australian Monsoonal tropics remains poorly understood. Of particular note (and in contrast to many other tropical regions in both Australia and elsewhere) is the current paucity of evidence for diverse endemic radiations of restricted-range taxa. Aims To use recently collected material from major surveys of the Kimberley Islands, Western Australia, to expand on a previous study that provided preliminary evidence of very high levels of geographically structured phylogenetic diversity in a lineage of tiny geckos (Crenadactylus). Methods Mitochondrial (ND2) and nuclear (RAG-1) sequence data were used to estimate the relationships, phylogenetic diversity and timescale of diversification of all populations of Crenadactylus from northern Australia from which samples for genetic analysis were available. Key results In striking contrast to the two subspecies currently recognised in the Kimberley, our analyses confirm the existence of a notable diversity of highly divergent and apparently allopatric lineages within the Kimberley, including at least 10 that are estimated to date to the late Pliocene/early Miocene (or earlier) and seven that we recognise as candidate new species. Most of this diversity is concentrated in the high-rainfall zone along the western edge of the Kimberley. Key conclusions A growing number of genetic datasets are revealing northern Australian vertebrate clades characterised by the juxtaposition of deeply divergent and highly geographically structured genetic diversity on the one hand, and major geographic gaps in sampling that impede full assessment of the distribution and taxonomic significance of this diversity on the other. Implications There is a pressing need for further surveys, voucher material and phylogenetic analyses to allow us to properly understand the diversity, biogeography and conservation needs of the northern Australian biota.

Ant-nest ichnofossils in honeycomb calcretes, Neogene Ogallala Formation, High Plains region of western Kansas, U.S.A.

Two new ant-nest trace fossils are described from calcic sandy paleosols of the Neogene Ogallala Formation in western Kansas. The ichnofossils are preserved within and below calcrete beds weathering in positive relief as carbonate-filled casts or as cavities in negative relief. Daimoniobarax ichnogenus nov. is established for burrow systems composed of vertically tiered, horizontally oriented pancake-shaped chambers connected by predominantly vertical and cylindrical shafts ~ 0.8 cm in diameter. Ichnospecies of Daimoniobarax are differentiated based on differences in the plan view outline of chambers, shaft orientation, and junctions between chambers and shafts. Daimoniobarax nephroides ichnospecies nov. is composed of an ~ 24–76 cm long vertical sequence of distinctly lobed chambers (~ 2–20 cm wide and ~ 1 cm high) arranged along sinuous to helical shafts. Chamber shape in plan view ranges from small teardrops to larger kidney- and U-shaped forms. Shafts intersect at chamber edges such that chambers appear to bud from the central shafts. Daimoniobarax nephroides is most similar to the nests of extant seed-harvester ants of the New World genus Pogonomyrmex. Such ants are specialized granivores and prefer sandy soils in arid to semi-arid grassland and desert regions. Daimoniobarax tschinkeli ichnospecies nov. is ~ 30–80 cm in vertical extent. Chambers (~ 2–30 cm wide and ~ 1 cm high) are circular to elongate or pseudopodial in plan view. Vertical shafts are straight to slightly sinuous and intersect most often toward the center of the chambers. The generalized architecture of D. tschinkeli is similar to that of the nests or nest portions of several extant ant genera, though it does not closely resemble any known modern nest. Ant ichnofossils provide valuable information on hidden biodiversity, paleohydrologic regimes, paleopedogenic processes, and paleoclimate during the time of nest occupation. Depth-related changes in chamber size and vertical spacing may also help interpret paleosurfaces and paleodepths, and serve as geopetal features.

ALIEN INVASIVE PATHOGENS: THE MAJOR THREAT TO OUR FOREST ECOSYSTEMS IN A TIME OF RAPID CLIMATE CHANGE

Forest ecosystems face unprecedented challenges from the rising rate of influx of alien invasive pests and pathogens resulting from increased global trade. Moreover, climate change predictions suggest that many additional alien pests and pathogens may become problems in forests as temperatures increase and rainfall patterns change. Recent indications of the potential for pathogens to transfer between hosts and the inter-specific hybridisation possible between related pathogens increase concerns over the possibility of escalations in damage in the future. Why are these organisms such a threat? Using examples drawn from wide-scale environmental damage caused to tree populations and forest ecosystems in Europe and elsewhere in the world, in this talk, we will illustrate the potential of alien pathogens to reduce biodiversity, alter ecosystems beyond recognition and impact on human requirements of forests. Classic examples of devastation by alien invasive pathogens affecting trees include Dutch elm disease, caused by Ophiostoma novo-ulmi, Jarrah dieback caused by Phytophthora cinnamomi, canker stain disease of Platanus caused by Ceratocystis platani, and white pine blister rust arising from accidental trans-Atlantic transfer of Cronartium ribicola. Many other examples exist in Europe and elsewhere in the world. Each of these pathogens still causes severe ecosystem damage in areas of introduction. Recent findings obtained from the application of state-of-the-art tools in molecular biology are reshaping our knowledge of alien invasive pathogens. The advent of these molecular biological techniques has greatly enhanced our ability to analyse aspects related to the biology, taxonomy, hidden biodiversity and temporal and spatial structuring of genetic diversity in organisms. Molecular diagnostic assays have resulted in improved detection methods for pests and pathogens based on molecular profiles, that are essential for accurate and rapid detection and enhanced understanding of the pathways of dispersal locally and internationally. This information greatly increases the reliability of pest risk assessment procedures and the development of phytosanitary measures aimed at eradicating, containing or managing these pests. The possibility of regulating the ‘plants for planting’ pathway, one of the major routes through which alien invasive problems are now entering and being dispersed in Europe, will be discussed.

Phenotypic evidence for hidden biodiversity in the Merodon aureus group (Diptera, Syrphidae) on the Balkan Peninsula: conservation implication

Cryptic species and phenotypic divergent units provided useful information about hidden biodiversity in the Merodon genus (Diptera, Syrphidae) on the Balkan Peninsula. Discrimination three cryptic species within both the M. aureus (M. aureus A, M. aureus B and M. aureus C) and M. cinereus (M. cinereus A, M. cinereus B and M. cinereus C) complexes was done by study of subtle wing variation (wing size and shape) using a geometric morphometric approach. Observed interspecific differentiation is generally in agreement with a previous study using molecular markers (allozyme loci, COI mtDNA). A considerable evolutionary and phenotypic intraspecies diversity of the M. aureus A, M. aureus B, M. aureus C, M. cinereus A, M. cinereus B, M. cinereus C and M. funestus species from the Balkan Peninsula has important implications for diagnosing biodiversity, including endemic and cryptic species. Observed phenotypic divergent units within the species might be considered as an evolutionary potential of the M. aureus group and used for defining conservation priorities. This study has contributed to the recognition of the value of wing traits in order to decipher the hidden diversity and evolutionary diversification.

“Problem Species” of the Savannah River Site, Such as Brimley's Chorus Frog (Pseudacris brimleyi), Demonstrate the Hidden Biodiversity Concept on an Intensively Studied Government Reserve

Abstract After more than five decades of intensive research on a wide variety of reptiles and amphibians at the Savannah River Site, the known occurrence of some members of the herpetofauna remains unresolved. One such “problem species,” Pseudacris brimleyi (Brimley's Chorus Frog), was recently found for the first time in over 50 years. The rediscovery of this cryptic species shows how the concept of hidden biodiversity not only applies to the general public, but to the scientific community as well.

Microinvertebrate and plant beta diversity in dry soils of a semiarid agricultural wetland complex

The relationship between environmental features and the β diversity of the propagule bank of dry soils of temporary wetlands has relevance to ecological theories of community structure and to the conservation of wetland biodiversity. The correlation of β diversity of microinvertebrates and macrophytes derived from propagules in dry soils with wetland habitat characteristics, catchment land-use, and the distance between wetlands in a remnant pond complex in central Spain was assessed. Redundancy analyses showed that β diversity of both groups correlated with habitat characteristics, whereas associations with catchment agricultural practices were weaker. Nestedness analyses showed that species-poor communities from degraded sites tended to form nested subsets of less degraded ponds with higher species richness. Distance between the ponds had no significant association with community similarity, suggesting that fragmentation did not shape β diversity at the scale of our study area. To maintain high β diversity in this area, ponds with species-rich propagule banks should receive conservation priority. Given the functional dependence by much wildlife on these propagule banks once these wetlands rewet, conservation of this hidden biodiversity is crucial for providing ecosystem services to humans and wildlife.

Four genes, morphology and ecology: distinguishing a new species of Acesta (Mollusca; Bivalvia) from the Gulf of Mexico

There is currently an active scientific debate about the most correct and efficient way to identify species. To date, few studies in the marine realm have combined the available taxonomic methods. In this study we have used morphology, ecology and molecular analyses to identify a new species within the bivalve genus Acesta. All four genes studied (12S, 16S, Cytb, COI) suggested that a common cold-seep species in the Gulf of Mexico, A. bullisi, should be divided into two distinct species. This conclusion was supported by morphological traits and by observations of ecological distribution. A. oophaga Jarnegren, Schander and Young n. sp. is described here, and A. bullisi Vokes (Tulane Stud Geol 2:75–92, 1963) is re-described. This study shows that DNA barcoding in combination with traditional morphological and ecological analyses may be an important tools to identify hidden biodiversity among deep-water organisms such as bivalves.

Hidden biodiversity in the groundwater of the Danube Flood Plain National Park (Austria)

A high number of stygobites (35 taxa) was recorded within a protected area, the Lobau in Vienna. It is shown that within National Parks, the identification of biodiversity hotspots of stygobites represents an attractive scientific activity, which increases the cultural value of protected landscapes.

Hidden biodiversity: detection of cryptic thynnine wasp species using sexually deceptive female–mimicking orchids

Hidden biodiversity: detection of cryptic thynnine wasp species using sexually deceptive female–mimicking orchids