Priority areas of intraspecific diversity: Larzac, a global hotspot for facultative paedomorphosis in amphibians

Although the designation of biodiversity hotspots is a valuable tool to improve conservation efforts, this is a concept primarily based on species diversity. In consequence, another component of biodiversity, adaptive variation, is often ignored in conservation and to my knowledge no attempt has been made to identify hotspots of remarkable intraspecific patterns. My aim was to focus on the process of facultative paedomorphosis (i.e. the retention of larval traits such as gills in adult variants), a rare developmental pathway. One hundred and seventy-four ponds were inventoried in Larzac (France) to determine the distribution and abundance of paedomorphic palmate newts Triturus helveticus (Amphibia, Caudata) and to compare these results with the current distribution of paedomorphs in this and other species. During this study, paedomorphic newts were found in 46 ponds, 32 of which were described here for the first time. Seventy-nine per cent of known paedomorphic populations of this species were found there, whereas this area covers only 0.5% of the distribution area of the species. This represents the highest known density of facultatively paedomorphic populations, all species being considered. Because these populations face a high threat of disappearance, Larzac should be designated as an intraspecific biodiversity hotspot in order to protect adaptive intraspecific variation. Future conservation-oriented work should focus not only on species distributions but also on phenotypically diverse but spatially localized variation.     

Plant genetic diversity in the Canary Islands: a conservation perspective

The Canary Islands are an Atlantic volcanic archipelago with a rich flora of ～570 endemic species. The endemics represent ～40% of the native flora of the islands, and ～20% of the endemics are in the E (endangered) category of the International Union for Conservation of Nature. A review of allozyme variation in 69 endemic species belonging to 18 genera and eight families is presented. The average species-level genetic diversity (H(T)) at allozyme loci is 0.186, which is twice as high as the mean reported for endemics of Pacific archipelagos. Possible factors contributing to this higher diversity are discussed, but the reasons remain obscure. An average of 28% of the allozyme diversity within species resides among populations, indicating a high level of interpopulational differentiation. Studies of reproductive biology indicate that many of the endemic species are outcrossers. The high total diversity within species, the relatively high differentiation among populations, and the outcrossing breeding systems have implications for species conservation. Decreased population sizes in outcrossing species would promote biparental inbreeding and increase inbreeding depression. The relatively high proportion of allozyme diversity among populations indicates that the most effective strategy for preserving genetic variation in species is to conserve as many populations as possible. The genetic diversity in many Canary Island endemics is endangered by: (1) overgrazing by introduced animals, such as barbary sheep, goats, mouflons, rabbits, and sheep; (2) interspecific hybridization following habitat disturbance or planting of endemics along roadsides or in public gardens; (3) competition with alien plant species; and (4) decline of population size because of urban development and farming.     

Birth of a hotspot of intraspecific genetic diversity: notes from the underground

Hotspots of intraspecific diversity have been observed in most species, often within areas of putative Pleistocene refugia. They have thus mostly been viewed as the outcome of prolonged stability of large populations within the refugia. However, recent evidence has suggested that several other microevolutionary processes could also be involved in their formation. Here, we investigate the contribution of these processes to current range-wide patterns of genetic diversity in the Italian endemic mole Talpa romana, using both nuclear (30 allozyme loci) and mitochondrial markers (cytochrome b sequences). Southern populations of this species showed an allozyme variation that is amongst the highest observed in small mammals (most populations had an expected heterozygosity of 0.10 or above), which was particularly unexpected for a subterranean species. Population genetic, phylogeographic and historical demographic analyses indicated that T. romana populations repeatedly underwent allopatric differentiations followed by secondary admixture within the refugial range in southern Italy. A prolonged demographic stability was reliably inferred from the mitochondrial DNA data only for a population group located north and east of the Calabrian peninsula, showing comparatively lower levels of allozyme variability, and lacking evidence of secondary admixture with other groups. Thus, our results point to the admixture between differentiated lineages as the main cause of the higher levels of diversity of refugial populations. When compared with the Pleistocene evolutionary history recently inferred for species from both the same and other geographic regions, these results suggest the need for a reappraisal of the role of gene exchange in the formation of intraspecific hotspots of genetic diversity.     

The role of waterholes as 'refugia' in sustaining genetic diversity and variation of two freshwater species in dryland river systems (Western Queensland, Australia)

1. Episodic floods and extended low or no flow periods characterise dryland river systems in Western Queensland, Australia. During protracted intervals between floods, rivers consist of a series of isolated waterholes, which serve as ‘refugia’ for aquatic species and much of the channel is dry. We categorised these waterholes into ‘main waterholes’, which are located in the main part of the river channel and ‘satellite waterholes’, which are located in distributary river channels. 2. We used mitochondrial sequences and allozymes to investigate levels of genetic diversity and patterns of connectivity among waterholes for two obligate freshwater species: Macrobrachium australiense (Decapoda: Palaemonidae) and Notopala sublineata (Gastropoda: Viviparidae). 3. We sampled 31 waterholes for M. australiense and 12 for N. sublineata. Based on a 505‐bp fragment of cytochrome oxidase subunit I, we identified 54 haplotypes in a sample of 232 individuals for M. australiense and based on a 457‐bp fragment of the same gene, 36 haplotypes in a sample of 145 individuals for N. sublineata. 4. Both nuclear and mitochondrial genetic data sets indicated that estimates of genetic diversity were not different in populations inhabiting main and satellite waterholes for either species. Also, there was generally very limited genetic differentiation among populations at any site. 5. We suggest that levels of connectivity among populations inhabiting waterholes at most sites are higher than expected. High levels of connectivity may help to maintain overall high levels of genetic diversity as well as low levels of genetic differentiation among waterholes within sites.     

Molecular taxonomic identification in the absence of a ‘barcoding gap’: a test with the endemic flora of the Canarian oceanic hotspot

We use a comprehensive subset of Canarian angiosperms corresponding to 23 families, 35 genera and 60 Canarian endemic taxa to test whether this flora is suitable to taxonomic identification with the two proposed plant DNA barcode sequences and whether these sequences may reveal the existence of cryptic species overlooked by morphology. The rate of discrimination success between the insular congeneric samples using the rbcL+matK combination and a ‘character‐based’ approach (where we use only the combination of nucleotide positions in an alignment that allows unambiguous species identification) is higher (82.29%) than that obtained with the ‘distance‐based’ approach (80.20%) used by the CBOL Plant Working Group in 2009 and also when compared with tests conducted in other floras. This suggests that the molecular identification of the Canarian endemic flora can be achieved as successfully as in other floras where the incidence of radiation is not as relevant. The facts that (i) a distance‐based criterion was unable to discriminate between congeneric and conspecific comparisons and (ii) only the character‐based discrimination criterion resolved cases that the distance‐based criterion did not, further support the use of a character discrimination approach for a more efficient DNA barcoding of floras from oceanic islands like the Canaries. Thus, a barcoding gap seems not to be necessary for the correct molecular characterization of the Canarian flora. DNA barcodes also suggest the possible existence of cryptic taxa to be further investigated by morphology and that the current taxonomic status of some of the taxa analysed may need revision.     

Amplification of multiple copies of mitochondrial Cytochrome b gene fragments in the Australian freshwater crayfish,Cherax destructor Clark (Parastacidae: Decapoda)

Non-coding copies of fragments of the mitochondrial genome translocated to the nucleus or pseudogenes are being found with increasing frequency in a diversity of organisms. As part of a study to evaluate the utility of a range of mitochondrial gene regions for population genetic and systematic studies of the Australian freshwater crayfish, Cherax destructor (the yabby), we report the first detection of Cytochrome b (Cyt b) pseudogenes in crustaceans. We amplified and sequenced fragments of the mitochondrial Cyt b gene from 14 individuals of C. destructor using polymerase chain reaction (PCR) with primers designed from conserved regions of Penaeus monodon and Drosophila melanogaster mitochondrial genomes. The phylogenetic tree produced from the amplified fragments using these primers showed a very different topology to the trees obtained from sequences from three other mitochondrial genes, suggesting one or more nuclear pseudogenes have been amplified. Supporting this conclusion, two highly divergent sequences were isolated from each of two single individuals, and a 2 base pair (bp) deletion in one sequence was observed. There was no evidence to support inadvertent amplification of parasite DNA or contamination of samples from other sources. These results add to other recent observations of pseudogenes suggesting the frequent transfer of mitochondrial DNA (mtDNA) genes to the nucleus and reinforces the necessity of great care in interpreting PCR-generated Cyt b sequences used in population or evolutionary studies in freshwater crayfish and crustaceans more generally.     

Species distributions represent intraspecific genetic diversity of freshwater fish in conservation assessments

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Environmental variation and rivers govern the structure of chimpanzee genetic diversity in a biodiversity hotspot

Background

The mechanisms that underlie the diversification of tropical animals remain poorly understood, but new approaches that combine geo-spatial modeling with spatially explicit genetic data are providing fresh insights on this topic. Data about the diversification of tropical mammals remain particularly sparse, and vanishingly few opportunities exist to study endangered large mammals that increasingly exist only in isolated pockets. The chimpanzees of Cameroon represent a unique opportunity to examine the mechanisms that promote genetic differentiation in tropical mammals because the region is home to two chimpanzee subspecies: Pan troglodytes ellioti and P. t. trogolodytes. Their ranges converge in central Cameroon, which is a geographically, climatically and environmentally complex region that presents an unparalleled opportunity to examine the roles of rivers and/or environmental variation in influencing the evolution of chimpanzee populations.

Results

We analyzed microsatellite genotypes and mtDNA HVRI sequencing data from wild chimpanzees sampled at a fine geographic scale across Cameroon and eastern Nigeria using a spatially explicit approach based upon Generalized Dissimilarity Modeling. Both the Sanaga River and environmental variation were found to contribute to driving separation of the subspecies. The importance of environmental variation differed among subspecies. Gene-environment associations were weak in P. t. troglodytes, whereas environmental variation was found to play a much larger role in shaping patterns of genetic differentiation in P. t. ellioti.

Conclusions

We found that both the Sanaga River and environmental variation likely play a role in shaping patterns of chimpanzee genetic diversity. Future studies using single nucleotide polymorphism (SNP) data are necessary to further understand how rivers and environmental variation contribute to shaping patterns of genetic variation in chimpanzees.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-014-0274-0) contains supplementary material, which is available to authorized users.     

Beta diversity of orchid bees in a tropical biodiversity hotspot

A controversial issue in ecology and conservation is whether community composition is controlled by niche or dispersal assembly. We assessed the importance of climatic factors and geographic gradients on the distribution of orchid bees in a severely-fragmented and species-rich tropical forest region in Brazil. Orchid-bee males were attracted to 17 different scent baits and collected in 15 forest sites. In total we captured 11,081 bees from 40 species. Climatic variables explained twice as much of the observed variation in the bee species data set as did pure spatial variation. However, most of the climatic explained variation was spatially structured, indicating that the species and the climatic data have a similar spatial arrangement. In fact, part of the observed latitudinal changes in community composition appears to be explained by a concomitant gradient in precipitation seasonality. Similarly, reduced temperatures and a more seasonal precipitation may help to explain the relative distinctiveness of the fauna from some of the westernmost sites. The level of similarity among the sampled sites, although highly variable, decayed both as function of the climatic and geographic distances among these sites. The greatest pairwise dissimilarities in the composition of the orchid-bee fauna were observed among sites 200–300 km from each other, since in many case those sites were more dissimilar in terms of climate than those further apart. It is suggested that global warming and consequent altered climatic regimes will influence the distribution patterns of orchid bees in a region already threatened by deforestation and forest fragmentation.     

Disentangling environmental correlates of vascular plant biodiversity in a Mediterranean hotspot

We determined the environmental correlates of vascular plant biodiversity in the Baetic‐Rifan region, a plant biodiversity hotspot in the western Mediterranean. A catalog of the whole flora of Andalusia and northern Morocco, the region that includes most of the Baetic‐Rifan complex, was compiled using recent comprehensive floristic catalogs. Hierarchical cluster analysis (HCA) and detrended correspondence analysis (DCA) of the different ecoregions of Andalusia and northern Morocco were conducted to determine their floristic affinities. Diversity patterns were studied further by focusing on regional endemic taxa. Endemic and nonendemic alpha diversities were regressed to several environmental variables. Finally, semi‐partial regressions on distance matrices were conducted to extract the respective contributions of climatic, altitudinal, lithological, and geographical distance matrices to beta diversity in endemic and nonendemic taxa. We found that West Rifan plant assemblages had more similarities with Andalusian ecoregions than with other nearby northern Morocco ecoregions. The endemic alpha diversity was explained relatively well by the environmental variables related to summer drought and extreme temperature values. Of all the variables, geographical distance contributed by far the most to spatial turnover in species diversity in the Baetic‐Rifan hotspot. In the Baetic range, climate was the most significant driver of nonendemic species beta diversity, while lithology and climate were the main drivers of endemic beta diversity. Despite the fact that Andalusia and northern Morocco are presently separated by the Atlantic Ocean and the Mediterranean Sea, the Baetic and Rifan mountain ranges have many floristic similarities – especially in their western ranges – due to past migration of species across the Strait of Gibraltar. Climatic variables could be shaping the spatial distribution of endemic species richness throughout the Baetic‐Rifan hotspot. Determinants of spatial turnover in biodiversity in the Baetic‐Rifan hotspot vary in importance between endemic and nonendemic species.     

Conservation of invertebrate biodiversity on a mountain in a global biodiversity hotspot,Cape Floral Region

Mountains present particular challenges for biodiversity conservation. Table Mountain is a significant mountain in a global biodiversity hotspot, the Cape Floristic Region. It has outstanding angiosperm diversity and endemism. Yet, aerial and foliage invertebrates in the area have been poorly studied, despite their importance as pollinators and predators. These plant and invertebrate assemblages are under great pressure from human disturbance. Aerial and foliage invertebrates were sampled with a range of techniques. Sites were chosen to make comparisons between vegetation structure and type, elevation and aspect. In total, 216 species from 63 families and 14 orders were recorded. Vegetation structure (fynbos or forest) and elevation were the most important environmental variables for both aerial and foliage invertebrates. Peak time for aerial invertebrate abundance was spring and summer in the fynbos and spring in the forests, while the foliage invertebrates showed very little seasonal variation. There was no correlation between the diversity of aerial and foliage invertebrates. When these results were compared with others on epigaeic invertebrates, it became clear that epigaeic and aerial invertebrates are not correlated, while epigaeic and foliage invertebrates were only partially correlated, but not sufficiently so to consider one as a reliable estimator of the other. The management pointer from this study is that sites at all elevations are vital for the conservation of biodiversity on Table Mountain. Both the aerial and epigaeic/foliage invertebrate assemblages will need to be monitored separately to maintain the mountain’s conservation status.     

Patterns of molecular evolution and diversification in a biodiversity hotspot: the California Floristic Province

The California Floristic Province harbours more endemic plant and animal taxa and more identifiable subspecies than any other area of comparable size in North America. We present evidence that physical historical processes have resulted in congruent patterns of genetic diversity over the past 2-10 million years. Using a molecular clock approach we show that diversification and establishment of spatial genetic structure across six taxonomic groups coincide with the putative age of California's mountain ranges and aridification in the region. Our results demonstrate the importance of geographical barriers and climatological events to species diversification and the overall geographical structure of biodiversity. These results should facilitate conservation efforts in this biodiversity hotspot for taxa whose population genetic structure is still unknown and may suggest the potential utility of this approach in regional conservation planning efforts.     

Palaeo‐islands as refugia and sources of genetic diversity within volcanic archipelagos: the case of the widespread endemic Canarina canariensis (Campanulaceae)

Geographical isolation by oceanic barriers and climatic stability has been postulated as some of the main factors driving diversification within volcanic archipelagos. However, few studies have focused on the effect that catastrophic volcanic events have had on patterns of within‐island differentiation in geological time. This study employed data from the chloroplast (cpDNA haplotypes) and the nuclear (AFLPs) genomes to examine the patterns of genetic variation in Canarina canariensis, an iconic plant species associated with the endemic laurel forest of the Canary Islands. We found a strong geographical population structure, with a first divergence around 0.8 Ma that has Tenerife as its central axis and divides Canarian populations into eastern and western clades. Genetic diversity was greatest in the geologically stable ‘palaeo‐islands’ of Anaga, Teno and Roque del Conde; these areas were also inferred as the ancestral location of migrant alleles towards other disturbed areas within Tenerife or the nearby islands using a Bayesian approach to phylogeographical clustering. Oceanic barriers, in contrast, appear to have played a lesser role in structuring genetic variation, with intra‐island levels of genetic diversity larger than those between‐islands. We argue that volcanic eruptions and landslides after the merging of the palaeo‐islands 3.5 Ma played key roles in generating genetic boundaries within Tenerife, with the palaeo‐islands acting as refugia against extinction, and as cradles and sources of genetic diversity to other areas within the archipelago.     

Artificial ponds increase local dragonfly diversity in a global biodiversity hotspot

Human demands have led to an increased number of artificial ponds for irrigation of crops year-round. Certain insect species have established in these ponds, including dragonflies (Insecta: Odonata). There has been discussion around the value of artificial ponds for encouraging dragonfly diversity, with little work in biodiversity hotspots rich in rare and endemic species. We focus here on the Cape Floristic Region (CFR) global biodiversity hotspot, which has many endemic dragonfly species but has few natural ponds. Yet it has many artificial ponds mostly used for irrigation on local farms. This leads to an interesting question: to what extent do these artificial ponds provide habitats for dragonflies in this biologically rich, agriculturally fragmented landscape? To answer this, we recorded dragonfly species richness and abundances from 17 artificial ponds and 13 natural stream deposition pools as reference, in an area of the CFR where there are no local, natural, perennial ponds. Thirteen environmental and physical variables were recorded at the ponds and pools. We found that although ponds attracted no rare or threatened dragonfly species, they increased the area of occupancy and population sizes of many generalist species. These came from nearby natural deposition pools or from unknown sources elsewhere in the region, so providing refuges which otherwise would not be there. Interestingly, some CFR endemic species were also recorded at our artificial ponds. Overall dragonfly assemblages and those of true dragonflies (Anisoptera) and damselflies (Zygoptera) differed between artificial ponds and deposition pools, suggesting that artificial ponds are to some extent a novel ecosystem. Habitat type, elevation and temperature were significant drivers in structuring overall species assemblages. For the Anisoptera, riparian vegetation and level of landscape connectivity was important, while temperature was not. In contrast, Zygoptera species were most affected by river catchment, habitat type and temperature. In sum, these artificial ponds are stepping stone habitats across an increasingly fragmented landscape. Managing these ponds with perennial water, constant water levels, and maximum complexity and heterogeneity of habitats in terms of vegetation will conserve a wide range of generalists and some specialists.     

Conservation threats and future prospects for the freshwater fishes of Ecuador: A hotspot of Neotropical fish diversity

Freshwater fish communities in Ecuador exhibit some of the highest levels of diversity and endemism in the Neotropics. Unfortunately, aquatic ecosystems in the country are under serious threat and conditions are deteriorating. In 2018–19, the government of Ecuador sponsored a series of workshops to examine the conservation status of Ecuador's freshwater fishes. Concerns were identified for 35 species, most of which are native to the Amazon region, and overfishing of Amazonian pimelodid catfishes emerged as a major issue. However, much of the information needed to make decisions across fish groups and regions was not available, hindering the process and highlighting the need for a review of the conservation threats to Ecuador's freshwater fishes. Here, we review how the physical alteration of rivers, deforestation, wetland and floodplain degradation, agricultural and urban water pollution, mining, oil extraction, dams, overfishing, introduced species and climate change are affecting freshwater fishes in Ecuador. Although many of these factors affect fishes throughout the Neotropics, the lack of data on Ecuadorian fish communities is staggering and highlights the urgent need for more research. We also make recommendations, including the need for proper enforcement of existing environmental laws, restoration of degraded aquatic ecosystems, establishment of a national monitoring system for freshwater ecosystems, investment in research to fill gaps in knowledge, and encouragement of public engagement in citizen science and conservation efforts. Freshwater fishes are an important component of the cultural and biological legacy of the Ecuadorian people. Conserving them for future generations is critical.     

Genetic diversity in populations of a freshwater ciliate

RAPD fingerprinting with nine different primers revealed that all of 18 E. aediculatus isolates from nine ponds and streams in western Germany, France and the U.S.A. were genetically different. The extent of genetic similarity between genotypes from different waters did not show a significant relationship with the geographical distance among habitats, although genotypes isolated from the same habitat showed a higher genetic similarity than genotypes isolated from different habitats. Phylogenetic analyses of RAPD patterns indicate a separation of E. aediculatus strains into subgroups within one species, but all strains were genetically more similar to one another than to strains from two other Euplotes species. Crossings of the different E. aediculatus strains revealed they belonged to seven mating types of one gene pool. The high genetic diversity observed is explained by a frequent occurrence of conjugation in the studied populations.     

淡水螯虾生理生态学与环境毒理学研究进展

综述了我国2种主养的淡水螯虾(克氏原螯虾和红螯螯虾)在生理生态学与环境毒理学方面的研究进展。总结了淡水螯虾的环境条件(盐度、温度和pH)适应范围、毒性污染物(氨氮、亚硝酸盐、重金属和农药等)的半致死浓度和安全浓度,以及环境胁迫和毒性污染物暴露对淡水螯虾生长、组织结构、生理代谢和免疫功能等的影响,为淡水螯虾养殖的水环境监测与调控提供参考依据。     

Fish fauna of Chalakudy River,part of Western Ghats biodiversity hotspot,Kerala, India: patterns of distribution,threats and conservation needs

Seventy one fish species belonging to 27 families and 50 genera were collected from various sampling sites spread along the upstream and downstream parts of the Chalakudy river, in the Western Ghats biodiversity hotspot in Kerala, South India. Cyprinids were the most dominant group represented by 24 species belonging to 13 genera, followed by the catfishes of the family Bagridae (7 species from 2 genera) and loaches belonging to the family Balitoridae (5 species from 5 genera). Of the 71 species, 4 belong to the ‘critically endangered’ (CR) and 16 to the ‘endangered’ (EN) category. 3 of the critically endangered species are strictly endemic to the Chalakudy river system. We also collected 5 exotic species several of them categorized as potential pest. Fish species richness (FSR) showed a direct relationship with increasing stream order with maximum values observed in the downstream/low elevation regions. Considerable differences were observed in the FSR between different microhabitats with maximum values observed in bed rock and pool riffle and the lowest in regimes followed by step pools. Diversity and species richness decreased with increasing altitude and higher diversity and species richness were observed in sampling sites located between 0–200 m above sea level. A definite temporal partitioning was also observed with regard to FSR with higher richness during the day time and the lowest observed at dawn. Indiscriminate collection of endemic and threatened ornamental fish species for export, exploitation of endangered food fishes by forest-dwelling communities and local fisher folk, pollution, loss of riparian cover, damming and exotic species threaten the rich ichthyofaunal diversity of Chalakudy River. An urgent need exists for studying the life history traits and demography of the most important endemic and threatened fishes, as lack of information on these aspects have significantly affected conservation efforts. The implementation of strong management strategies like fixing total allowable catch (TAC), and the use of quotas are needed to reduce the overall collection pressure with regard to the trade in native ornamental species from the river.