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 population divergence and speciation. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 391–403.     

Cryptic species complexes,widespread species and conservation: lessons from Amazonian frogs of the Leptodactylus marmoratus group (Anura: Leptodactylidae)

Morphologically cryptic species act as a wild card when it comes to biodiversity assessments and conservation, with the capacity to dramatically alter our understanding of the biological landscape at the taxonomic, ecological, biogeographic, evolutionary, and conservation levels. We discuss the potential effects that cryptic species may have on biodiversity assessments and conservation, as well as some of the current issues involving the treatment of cryptic species both at taxonomic and conservation levels. In addition, using a combination of advertisement call and morphological data, we describe a new species of the Leptodactylus marmoratus group from the upper Amazon basin, and we assess how cryptic species can affect conservation assessments of species in the Leptodactylus marmoratus group by examining how recent findings affect our understanding of the distribution of what is assumed to be a widespread Amazonian species, Leptodactylus andreae.     

Amphibian assemblages and diversity patterns in two forest ecosystems of South-Eastern Nigeria

Despite recent anthropogenic interference, south-eastern (SE) Nigeria historically hosts a myriad of pristine forest habitats that could sustain diverse amphibian assemblages. Currently, land conversion of primary forests through human activities has led to modified habitats, such as agricultural fields and secondary forest. This calls for biodiversity documentation and initiation of conservation plans. However, the dearth of herpetological studies has limited knowledge of the amphibian species richness and distribution patterns in some forest ecosystems of SE Nigeria. Thus, we surveyed two less-explored intact forests in SE Nigeria—Afi Forest Reserve (AFR) and Ikpan forest ecosystem (IFE)—to document the patterns of amphibian diversity and distribution. Specimens were searched for opportunistically using visual and acoustic survey methods. Literature searches were conducted to document additional species that were not encountered. Using the observational records and arrays of diversity indices, the patterns of species richness and abundance across habitat types were evaluated. The result of our study revealed the presence of 30 and 31 amphibian species from AFR and IFE, respectively. Our field collections included two unidentified species (Sclerophrys sp. and Hyperolius sp.) from AFR and one (Phrynobatrachus sp.) from IFE. Analyses revealed high species diversity and richness in forest and swamps compared with the agricultural field and savannah. Given the increased human activities and the antecedent threats to forest ecosystems of SE Nigeria, we offer recommendations for the initiation of conservation plans for these two surveyed localities.     

DNA barcodes for the pipefish genus Corythoichthys (Actinopterygii: Syngnathiformes) from the Indian Ocean provide insights into cryptic diversity

The syngnathiform genus Corythoichthys comprises a group of taxonomically complex, tail-brooding (Syngnathinae) pipefishes widely distributed in the Indo-Pacific region. Due to the presence of overlapping interspecific morphological characters, reliable taxonomic information on Corythoichthys is still lacking. Using 52 CO1 sequences, including seven newly generated, a phylogenetic analysis was carried out to understand the genetic diversity, distribution and ‘species groups’ within the genus Corythoichthys. Species delimitation using Automatic Barcode Gap Discovery (ABGD) analysis confirmed the presence of 13 species which include ‘species-complexes’ previously considered as a single taxon. Our results revealed the presence of three species groups, ‘C. amplexus’, ‘C. conspicillatus’ and ‘C. haematopterus’ and four unidentified/undescribed species in the wider Indo-Pacific realm. Interestingly, 60 sequences and a mitogenome identified as Corythoichthys in GenBank are misidentified at the genus level. Based on our findings, we suggest that the taxonomy and systematics of Corythoichthys need to be re-examined and validated using integrative methods, and care should be taken while selecting specimens for genetic studies.     

Global analysis reveals that cryptic diversity is linked with habitat but not mode of life

The ubiquity of genetically distinct, cryptic species is limiting any attempt to estimate local or global biodiversity as well as impeding efforts to conserve species or control pests and diseases. Environmental factors or biological traits promoting rapid diversification into morphologically similar species remain unclear. Here, using a meta‐analysis of 1230 studies using DNA sequences to search for cryptic diversity in metazoan taxa, we test two hypotheses regarding the frequency of cryptic taxa based on mode of life and habitat. First, after correcting for study effort and accounting for higher taxonomic affinities and biogeographical region of origins, our results do not support the hypothesis that cryptic taxa are more frequent among parasitic than free‐living taxa. Second, in contrast, the results support the hypothesis that cryptic taxa are more common in certain habitats than others: for a given study effort, more cryptic taxa are found in freshwater than in terrestrial or marine taxa. These findings suggest that the greater heterogeneity and fragmentation of freshwater habitats may promote higher rates of genetic differentiation among its inhabitants, a general pattern with serious implications for freshwater conservation biology.     

隐种及其在两栖动物中的研究进展

近年来,由于分子生物学的迅猛发展,物种内隐藏的生物多样性越来越多地被发现,由此引发的隐种问题也备受关注。隐种的存在对现有的生物多样性评估提出了挑战。在实践上,隐种的界定对于自然资源的保护和管理具有重要意义。两栖动物由于迁移能力较弱,通常具有较强的遗传分化,因而可能包含较丰富的隐种多样性。简述了隐种的概念和形成机制,归纳了国内外两栖类动物中隐种的研究进展,并着重介绍了界定两栖动物隐种的研究方法,最后,对今后两栖动物隐种的研究作了简要展望。我国两栖动物资源丰富,并具有独特的地形和气候特点,对这些物种遗传多样性和系统地理学的研究亟待开展。     

Importance of riparian remnants for frog species diversity in a highly fragmented rainforest

Tropical forests undergo continuous transformation to other land uses, resulting in landscapes typified by forest fragments surrounded by anthropogenic habitats. Small forest fragments, specifically strip-shaped remnants flanking streams (referred to as riparian remnants), can be particularly important for the maintenance and conservation of biodiversity within highly fragmented forests. We compared frog species diversity between riparian remnants, other forest fragments and cattle pastures in a tropical landscape in Los Tuxtlas, Mexico. We found similar species richness in the three habitats studied and a similar assemblage structure between riparian remnants and forest fragments, although species composition differed by 50 per cent. Frog abundance was halved in riparian remnants compared with forest fragments, but was twice that found in pastures. Our results suggest that riparian remnants play an important role in maintaining a portion of frog species diversity in a highly fragmented forest, particularly during environmentally stressful (hot and dry) periods. In this regard, however, the role of riparian remnants is complementary, rather than substitutive, with respect to the function of other forest fragments within the fragmented forest.     

Differential responses of cryptic bat species to the urban landscape

Urbanization is a key global driver in the modification of land use and has been linked to population declines even in widespread and relatively common species. Cities comprise a complex assortment of habitat types yet we know relatively little about the effects of their composition and spatial configuration on species distribution. Although many bat species exploit human resources, the majority of species are negatively impacted by urbanization. Here, we use data from the National Bat Monitoring Programme, a long‐running citizen science scheme, to assess how two cryptic European bat species respond to the urban landscape. A total of 124 × 1 km² sites throughout Britain were surveyed. The landscape surrounding each site was mapped and classified into discrete biotope types (e.g., woodland). Generalized linear models were used to assess differences in the response to the urban environment between the two species, and which landscape factors were associated with the distributions of P. pipistrellus and P. pygmaeus. The relative prevalence of P. pygmaeus compared to P. pipistrellus was greater in urban landscapes with a higher density of rivers and lakes, whereas P. pipistrellus was frequently detected in landscapes comprising a high proportion of green space (e.g., parklands). Although P. pipistrellus is thought to be well adapted to the urban landscape, we found a strong negative response to urbanization at a relatively local scale (1 km), whilst P. pygmaeus was detected more regularly in wooded urban landscapes containing freshwater. These results show differential habitat use at a landscape scale of two morphologically similar species, indicating that cryptic species may respond differently to anthropogenic disturbance. Even species considered relatively common and well adapted to the urban landscape may respond negatively to the built environment highlighting the future challenges involved in maintaining biodiversity within an increasingly urbanized world.     

Cultivated plant species diversity in home gardens of an Amazonian peasant village in Northeastern Peru

Research on agrobiodiversity points to the importance of home gardens in situ conservation, yet few studies to date explicate the origins and dynamics of plant species diversity. In this paper, we examine inter-household variations in cultivated plant species diversity among house gardens in a traditional peasant community, near Iquitos, Peru. In-depth household interviews (n = 24) and garden/field surveys reveal that home gardens are clearly the site of highest plant diversity in farmers’ field portfolios, and that substantial differences exist in garden composition, plant diversity, and the sources of garden planting material across households. Statistical analyses indicate that home garden diversity is related strongly to specific garden characteristics, household socioeconomic features, and access to planting material including seeds, cuttings, and suckers. The role and implications of differential access to planting material in the development and maintenance of crop species diversity is signaled as an important theme for future study in economic botany.     

DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species

There is currently international interest in the application of DNA barcoding as a tool for plant species discrimination and identification. In this study, we evaluated the utility of five candidate plant DNA barcoding regions [rbcL, matK, trnH-psbA, trnL-F and internal transcribed spacer (ITS)] in Eurasian yews. This group of species is taxonomically difficult because of a lack of clear-cut morphologically differences between species and hence represents a good test case for DNA barcoding. Forty-seven accessions were analysed, representing all taxa treated in current floristic works and covering most of the distribution range of Taxus in Eurasia. As single loci, trnL-F and ITS showed the highest species discriminatory power, each resolving 11 of 11 lineages (= barcode taxa). Species discrimination using matK, trnH-psbA and rbcL individually was lower, with matK resolving 8 of 10, trnH-psbA 7 of 11 and rbcL 5 of 11 successfully sequenced lineages. The proposed CBOL core barcode (rbcL + matK) resolved 8 of 11 lineages. Combining loci generally increased the robustness (measured by clade support) of the barcoding discrimination. Based on overall performance, trnL-F and ITS, separately or combined, are proposed as barcode for Eurasian Taxus. DNA barcoding discriminated recognized taxa of Eurasian Taxus, namely T. baccata, T. cuspidata, T. fuana and T. sumatrana, and identified seven lineages among the T. wallichiana group, some with distinct geographical distributions and morphologies, and potentially representing new species. Using the proposed DNA barcode, a technical system can be established to rapidly and reliably identify Taxus species in Eurasia for conservation protection and for monitoring illegal trade.     

中国佛教寺庙植物多样性和佛教树种替代

佛教是我国的主要宗教之一, 佛教寺庙作为佛教文化的物质载体, 对区域生物多样性的保护具有重要意义。本研究收集了中国191座寺庙的树种名录, 分析了不同地区寺庙的树种组成、分布格局及影响因素, 以明确寺庙在生物多样性保护中的作用。结果表明: (1)全国191座寺庙共收集到树种1,059种, 隶属116科410属, 大多数树种(773种)仅出现在1-2座寺庙中; (2)寺庙树种中含有大量乡土植物, 并且保存了丰富的受威胁树种(94种), 具有较高的生物多样性保护价值; (3)不同气候带的佛教树种组成差异较大, 主要受气候因子限制; (4)佛教树种具有清晰的树种替代现象, 由南向北原始佛教树种逐渐由形态相似的本土物种(替代佛教树种)替代。以上结果表明中国寺庙中保存了非常丰富的植物资源, 有效地保护和利用寺庙植物资源对维持区域生物多样性和提升城市绿化水平具有积极作用。     

福建省两栖类物种多样性评估

地区性物种多样性评价是当前全球生物多样性研究的重要组成部分。本文采用G-F指数对福建省两栖类物种多样性进行评估,同时利用弦距离类间平均连锁的方法对福建省22个县（市）和5个两栖动物地理省进行聚类分析。结果表时：福建省各县（市）的两栖类物种多样性差异较大,其中武夷山市两栖类物种多样性的G指数,F指数和G-F指数分别为2.978,4.863和0.388。处于华中区的3个地理省（闽北、闽东和闽西地理省）首先聚类,而后与处于华南区的闽中地理省聚类,最后与闽南地理省合并。聚类结果与福建省两栖动物地理区划大体一致,但个别县（市）不太相符,作者建议将大田县划归在华中区的闽西地理省。     

Morphological and molecular investigation of polymorphism and cryptic species in tanaid crustaceans: implications for tanaid systematics and biodiversity estimates

A combination of traditional taxonomic procedures and molecular techniques has provided new insight into the problems of cryptic species and sexual and ontogenetic polymorphism in the Tanaidacea. Using polymerase chain reaction and DNA markers, three cryptic species of Paratanais were identified. PCR primers were used to amplify the divergent internal transcribed spacers (ITS) of these species. Restriction digestion of the amplified rDNA generated species specific DNA banding. Male and five female stages of Paratanais maleticus sp. nov. and two other new species, P. malign us and P. perturbatius , are described. Morphological variation, both sexual and ontogenetic, was found in several generic characters of Paratanais and required the diagnosis to be modified. The identification of three undescribed cryptic species from a single microhabitat in a well studied, shallow water and easily accessible locality, demonstrate that the biodiversity of tanaid crustacean is significantly underestimated.     

High level of cryptic species diversity revealed by sympatric lineages of Southeast Asian forest frogs

Amphibians tend to exhibit conservative morphological evolution, and the application of molecular and bioacoustic tools in systematic studies have been effective at revealing morphologically 'cryptic' species within taxa that were previously considered to be a single species. We report molecular genetic findings on two forest-dwelling ranid frogs from localities across Southeast Asia, and show that sympatric evolutionary lineages of morphologically cryptic frogs are a common pattern. These findings imply that species diversity of Southeast Asian frogs remains significantly underestimated, and taken in concert with other molecular investigations, suggest there may not be any geographically widespread, forest-dwelling frog species in the region. Accurate assessments of diversity and distributions are needed to mitigate extinctions of evolutionary lineages in these threatened vertebrates.     

Geographical variation in the high-duty cycle echolocation of the cryptic common mustached bat Pteronotus cf. rubiginosus (Mormoopidae)

The use of bioacoustics as a tool for bat research is rapidly increasing worldwide. There is substantial evidence that environmental factors such as weather conditions or habitat structure can affect echolocation call structure in bats and thus compromise proper species identification. However, intraspecific differences in echolocation due to geographical variation are poorly understood, which poses a number of issues in terms of method standardization. We examined acoustic data for Pteronotus cf. rubiginosus from the Central Amazon and the Guiana Shield. We provide the first evidence of intraspecific geographic variation in bat echolocation in the Neotropics, with calls significantly differing in almost all standard acoustic parameters for the two lineages of this clade. We complement our bioacoustic data with molecular and morphological data for both species. Considerable overlap in trait values prevents reliable discrimination between the two sympatric Pteronotus based on morphological characters. On the other hand, significant divergence in the frequency of maximum energy suggests that bioacoustics can be used to readily separate both taxa despite extensive intraspecific variability in their echolocation across the Amazon. Given the relative lack of barriers preventing contact between bat populations from the Central Amazon and French Guiana, the documented acoustic variation needs to be further studied in geographically intermediate locations to understand the potential isolation processes that could be causing the described divergence in echolocation and to determine whether this variation is either discrete or continuous.     

Uneven distribution of cryptic diversity among higher taxa of parasitic worms

Cryptic species cause problems for estimates of biodiversity. In the case of parasites, cryptic species also plague efforts to detect potential zoonotic diseases or invasive pathogens. It is crucial to determine whether the likelihood of finding cryptic species differs among higher parasite taxa, to better calibrate estimates of diversity and monitor diseases. Using published reports of cryptic species of helminth parasites identified using molecular tools, I show that the number of species found is strongly related to the number of parasite individuals sequenced, weakly influenced by the number of host species from which parasites were obtained, and unaffected by the genetic markers used. After correction for these factors, more cryptic species of trematodes are found than in other helminth taxa. Although several features distinguish trematodes from other helminths, it is probable that our inability to discriminate among sibling species of trematodes results from their lack of structures serving as species-specific morphological markers. The available data suggest that current estimates of helminth diversity may need to be doubled (tripled for trematodes) to better reflect extant diversity.