Extensive intraspecific genetic diversity of a freshwater crayfish in a biodiversity hotspot

1. The freshwater crayfish Cherax dispar (Decapoda: Parastacidae) inhabits coastal regions and islands of South East Queensland, Australia. We hypothesised that populations of C. dispar on different islands would be more genetically divergent from each other than populations from different drainages within the same island or on the mainland. 2. Phylogenetic and phylogeographic analyses were conducted on two mitochondrial genes (cytochrome oxidase subunit I & 16S ribosomal DNA) and one nuclear gene (Internal Transcribed Spacer region 2). Phylogeographic patterns were compared with those for other freshwater organisms in the area. 3. Deep genetic divergences were found within C. dispar, including four highly divergent (up to 20%) clades. The geographic distribution of each of the clades revealed strong latitudinal structuring along the coast rather than structuring among the islands. The high genetic divergence observed among the C. dispar clades was estimated to have pre‐dated island formation and may represent ancient river drainage patterns. 4. A restricted distribution was observed for the most divergent clade, which was discovered only on two of the sand islands (North Stradbroke Island and Moreton Island). Furthermore, strong phylogeographic structuring was observed within this clade on North Stradbroke Island, where no haplotypes were shared between samples from opposite sides of the island. This low connectivity within the island supports the idea that C. dispar rarely disperse terrestrially (i.e. across watersheds).     

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.     

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.     

Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial

The extent of genetic diversity loss and former connectivity between fragmented populations are often unknown factors when studying endangered species. While genetic techniques are commonly applied in extant populations to assess temporal and spatial demographic changes, it is no substitute for directly measuring past diversity using ancient DNA (aDNA). We analysed both mitochondrial DNA (mtDNA) and nuclear microsatellite loci from 64 historical fossil and skin samples of the critically endangered Western Australian woylie (Bettongia penicillata ogilbyi), and compared them with 231 (n = 152 for mtDNA) modern samples. In modern woylie populations 15 mitochondrial control region (CR) haplotypes were identified. Interestingly, mtDNA CR data from only 29 historical samples demonstrated 15 previously unknown haplotypes and detected an extinct divergent clade. Through modelling, we estimated the loss of CR mtDNA diversity to be between 46% and 91% and estimated this to have occurred in the past 2000–4000 years in association with a dramatic population decline. In addition, we obtained near‐complete 11‐loci microsatellite profiles from 21 historical samples. In agreement with the mtDNA data, a number of ‘new’ microsatellite alleles was only detected in the historical populations despite extensive modern sampling, indicating a nuclear genetic diversity loss >20%. Calculations of genetic diversity (heterozygosity and allelic rarefaction) showed that these were significantly higher in the past and that there was a high degree of gene flow across the woylie's historical range. These findings have an immediate impact on how the extant populations are managed and we recommend the implementation of an assisted migration programme to prevent further loss of genetic diversity. Our study demonstrates the value of integrating aDNA data into current‐day conservation strategies.     

Environmental transition zone and rivers shape intraspecific population structure and genetic diversity of an Amazonian rain forest tree frog

Diversification processes acting across geographically continuous populations have been rarely documented in Amazonia, because of the lack of fine-scale sampling over extensive areas. We aimed to determine the geographic effects of an environmental transition zone and large rivers on the intraspecific population structure of the Manaus slender-legged tree frog (Osteocephalus taurinus) along a ~ 900 km transect of tropical rain forest. Using one mitochondrial (16S), two nuclear genes (TYR, POMC) and three microsatellites, we estimated the population structure, phylogenetic relationships and geographic variation of 262 O. taurinus and 5 O. oophagus (a close relative) along the Purus–Madeira interfluve (PMI) and opposite banks of the central Amazon and upper Madeira rivers, at central-southern Amazonia, Brazil. Six genetic clusters were identified: two corresponding to sympatric populations of O. taurinus and O. oophagus from their type locality, north of Amazon river. Within PMI, there were three distinct O. taurinus genetic clusters distributed along the geographic gradient with one main phylogeographic break found (concordant between 16S and TYR), that corresponds to a transition zone (ecotone) between dense and open rain forest ecotypes. The sixth cluster was an O. taurinus population isolated at the east bank of the upper Madeira river. In addition, restricted haplotype sharing was identified from the west to east banks at upper Madeira river. Within PMI, parapatric genetic structure is explained by a potential association of the genetic clusters to the different forest ecotypes they inhabit coupled with isolation by distance, thus supporting the gradient hypothesis for diversification. Differentiation of populations that are external to the PMI is most likely explained by the barrier effect of the Madeira and Amazon rivers. Our findings provide new evidence on diversification processes across continuous Amazonian landscapes; however, the specific mechanisms underlying the origin and maintenance of the identified phylogeographic break need to be further studied.     

Floristic diversity along the roadsides of an urban biodiversity hotspot in Indian Himalayas

In the urban landscapes, scientific understanding of the roadside vegetation is a prerequisite for better planning and designing of sustainable cities. The Srinagar city, located in the Indian Himalayas, represents an urban biodiversity hotspot but the information about the floristic diversity especially along its roadsides is lacking. In order to fill this knowledge gap, the present study using field-based plant collection surveys was undertaken to investigate the floristic diversity growing along the roadsides of Srinagar. A total of 206 vascular plant species were recorded with the proportion of alien species relatively higher (52%) than the native species (48%). Of the 108 alien species, 24 were invasive, 44 naturalized, 12 casual and 23 were cultivated. Most of the species were herbs (165 spp.) and the majority of these were wild growing (155 spp.). Based on Raunkiaer’s lifeform characterization, therophytes (94 spp.) were the most dominant. Interestingly, the therophytes harboured the highest number of alien species (50 spp.), followed by phanerophytes (29 spp.). There was significant difference between the floristic spectrum obtained during the present study and the normal Raunkiaer’s spectrum. The present study provides policy-relevant baseline data which can guide the urban planners to develop sustainable planning in this Himalayan city.     

Pattern and drivers of speciesgenetic diversity correlation in natural forest tree communities across a biodiversity hotspot

Aims Exploring species-genetic diversity correlation (SGDC) is essential for understanding spatial patterns of diversity and the underlying mechanisms. Until now, latitudinal patterns of species diversity (SD) and genetic diversity (GD) were rarely studied simultaneously. As the freezing-tolerance hypothesis predicts a decrease of SD from low to high latitudes and the central-marginal hypothesis predicts a unimodal pattern of GD along latitude, we hypothesized that SD and GD are uncorrelated. We also tested how climatic and edaphic factors affect the correlation between the two levels of biodiversity.     

Snakehead (Teleostei: Channidae) diversity and the Eastern Himalaya biodiversity hotspot

The collision of the Indian and Eurasian landmasses in the Cenozoic was a decisive factor in shaping biodiversity patterns in Southern and Southeastern Asia. While most studies thus far have focused on the biotic interchange between India and Eurasia and evolutionary diversification on or around the Tibetan Plateau, little attention has been paid to the biodiversity buildup in the Eastern Himalaya biodiversity hotspot (EHH) which harbors over 540 freshwater fish species with a high degree of endemicity. An important component of the regional ichthyofauna are snakehead fishes of the family Channidae comprising throughout their African-Asian distribution 47 valid species, but a poorly known species-level diversity. In order to evaluate channid intrarelationships and biogeography, a temporal and geographic framework of channid evolution in conjunction with a critical reevaluation of the channid fossil record is warranted. Based on molecular data, we provide a comprehensive species-level phylogeny based on 223 channid individuals belonging to 37 species and one additional currently undescribed species. The first split within channids separates the African genus Parachanna from the Asian genus Channa which can be divided into eight distinct species groups (Argus, Asiatica, Gachua, Lucius, Marulius, Micropeltes, Punctata, and Striata groups). Large intraspecific divergences were observed within several species and potentially indicate additional species-level diversity. Almost 40% of the channid species are narrow-range endemics belonging to the Gachua group. These are found in the EHH making this area an outstanding hotspot for endemic channid diversity. The large majority of the EHH endemics are restricted to the southern foothills of the Eastern Himalaya and the Shillong-Mikir Hills Plateau, areas west of the Indoburman Ranges. Our results reveal complex and difficult to interpret biogeographic patterns indicating that both vicariance and dispersal events have potentially been responsible in shaping current distribution patterns in Asian channids. We recognize †Parachanna fayumensis as the oldest reliable channid fossil and argue that the three oldest so-called channid fossils (i.e., †Eochanna chlorakkiensis, †Anchichanna kuldanensis, and †Ophiocephalus lydekkeri) lack clear diagnostic features that would allow them to be unequivocally placed within Channidae.     

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.     

Environmental and climatic determinants of molecular diversity and genetic population structure in a coenagrionid damselfly

Identifying environmental factors that structure intraspecific genetic diversity is of interest for both habitat preservation and biodiversity conservation. Recent advances in statistical and geographical genetics make it possible to investigate how environmental factors affect geographic organisation and population structure of molecular genetic diversity within species. Here we present a study on a common and wide ranging insect, the blue tailed damselfly Ischnuraelegans, which has been the target of many ecological and evolutionary studies. We addressed the following questions: (i) Is the population structure affected by longitudinal or latitudinal gradients?; (ii) Do geographic boundaries limit gene flow?; (iii) Does geographic distance affect connectivity and is there a signature of past bottlenecks?; (iv) Is there evidence of a recent range expansion and (vi) what is the effect of geography and climatic factors on population structure? We found low to moderate genetic sub-structuring between populations (mean F_ST = 0.06, D_est = 0.12), and an effect of longitude, but not latitude, on genetic diversity. No significant effects of geographic boundaries (e.g. water bodies) were found. F_ST-and D_est-values increased with geographic distance; however, there was no evidence for recent bottlenecks. Finally, we did not detect any molecular signatures of range expansions or an effect of geographic suitability, although local precipitation had a strong effect on genetic differentiation. The population structure of this small insect has probably been shaped by ecological factors that are correlated with longitudinal gradients, geographic distances, and local precipitation. The relatively weak global population structure and high degree of genetic variation within populations suggest that I. elegans has high dispersal ability, which is consistent with this species being an effective and early coloniser of new habitats.     

Comparative phylogeography reveals a shared impact of pleistocene environmental change in shaping genetic diversity within nine Anopheles mosquito species across the Indo-Burma biodiversity hotspot

South-East Asia is one of the world's richest regions in terms of biodiversity. An understanding of the distribution of diversity and the factors shaping it is lacking, yet essential for identifying conservation priorities for the region's highly threatened biodiversity. Here, we take a large-scale comparative approach, combining data from nine forest-associated Anopheles mosquito species and using statistical phylogeographical methods to disentangle the effects of environmental history, species-specific ecology and random coalescent effects. Spatially explicit modelling of Pleistocene demographic history supports a common influence of environmental events in shaping the genetic diversity of all species examined, despite differences in species' mtDNA gene trees. Populations were periodically restricted to allopatric northeastern and northwestern refugia, most likely due to Pleistocene forest fragmentation. Subsequent southwards post-glacial recolonization is supported by a north-south gradient of decreasing genetic diversity. Repeated allopatric fragmentation and recolonization have led to the formation of deeply divergent geographical lineages within four species and a suture zone where these intraspecific lineages meet along the Thai-Myanmar border. A common environmental influence for this divergence was further indicated by strong support for simultaneous divergence within the same four species, dating to approximately 900 thousand years ago (kya). Differences in the geographical structuring of genetic diversity between species are probably the result of varying species' biology. The findings have important implications for conservation planning; if the refugial regions and suture zone identified here are shared by other forest taxa, the unique and high levels of genetic diversity they house will make these areas conservation priorities.     

Searching for heat in a marine biodiversity hotspot

Coral reefs exhibit highly congruent patterns of biodiversity, with a prominent hotspot in the Indo-Australian Archipelago (IAA). Unlike many terrestrial systems, the IAA hotspot exhibits extensive latitudinal and longitudinal biodiversity gradients. Conflicting hypotheses have highlighted the importance of the area as a centre of origin, overlap or accumulation, with the location of endemics being used as the primary criterion for testing these hypotheses, by identifying the presumed geographical origins of species. We evaluate the utility of marine endemics for resolving these hypotheses, and examine recent molecular phylogenetic evidence for coral reef species that has revealed the antiquity of the endemics and the other species that make up this hotspot. These analyses emphasize the importance of the IAA in the survival rather than the origins of species.     

Population structure, genetic variation and morphological diversity in indigenous sheep of Ethiopia

We investigated genetic and morphological diversity and population structure of 14 traditional sheep populations originating from four ecological zones in Ethiopia (sub-alpine, wet highland, sub-humid lowland and arid lowland). All animals (n = 672) were genotyped for 17 microsatellite markers and scored for 12 morphological characters. The sheep were initially classified as fat-tailed (11 populations), thin-tailed (one population) and fat-rumped sheep (two populations). These classifications are thought to correspond to three consecutive introduction events of sheep from the Near-East into East Africa. For the 14 populations, allelic richness ranged from 5.87 to 7.51 and expected heterozygosity (H(E)) from 0.66 to 0.75. Genetic differentiations (F(ST) values) between all pairs of populations, except between sub-alpine populations, were significantly different from zero (P < 0.001). Cluster analysis of morphological characters and a dendrogram constructed from genetic distances were broadly consistent with the classification into fat-tailed, thin-tailed and fat-rumped sheep. Bayesian cluster analysis using microsatellite markers indicated that there has been further genetic differentiation after the initial introduction of sheep into Ethiopia. Investigation of factors associated with genetic variation showed that an isolation-by-distance model, independently of other factors, explained most of the observed genetic variation. We also obtained a strong indication of adaptive divergence in morphological characters, patterns of morphological variation being highly associated with ecology even when the effect of neutral genetic divergence (F(ST)) was parcelled out in partial Mantel tests. Using a combination of F(ST) values, Bayesian clustering analysis and morphological divergence, we propose a classification of Ethiopian sheep into six breed groups and nine breeds.     

Diversity patterns in a diversity hotspot

Our knowledge of diversity patterns is generally founded on studies performed in the more species‐poor part of our globe. Ibanez et al. (2014, this issue) report on patterns based on impressive field efforts in a diversity hotspot, namely New Caledonia. Some intriguing patterns arise from this study offering valuable insights in our quest to understand and manage global biodiversity.     

Species richness and phylogenetic diversity of different growth forms of angiosperms across a biodiversity hotspot in the horn of Africa

Woody and herbaceous plants are differentially influenced by the environment, with non‐random association with the evolutionary history of these taxa and their traits. In general, woody plants may have climate‐dominated niches, whereas herbaceous plants may have edaphic and microhabitat‐dominated niches. Here, we explored and mapped how the patterns of species richness, phylogenetic diversity, and structures of total, woody, and herbaceous plants vary across the geographical regions and with respect to 12 environmental variables across Ethiopia and Eritrea, in the horn of Africa. Our result showed that both richness and phylogenetic diversity had almost the same tendency in total woody and herbaceous plants, in which they showed positive relationships with annual precipitation, precipitation annual range of climate, all the three variables of topography, and total nitrogen and total extractable phosphorus of soil, and negative relations with mean annual temperature. Compared with the total and herbaceous plants, the environmental variables explained greater variance both in the standardized effect size phylogenetic diversity and net relatedness index for woody plants. Our results highlight that, on the large spatial scales, the environmental filtering process has played a greater role in structuring species into local communities for woody plants than for herbaceous plants.