Genetic variation of Parapenaeopsis sculptilis (Decapoda, Penaeidae) and reassessment of the phylogenetic relationships within the genus Parapenaeopsis based on mitochondrial DNA variation

The genus Parapenaeopsis is an important group of marine shrimps for wild capture in the Indo-West Pacific region. Phylogenetics of penaeid shrimps is still a debatable issue. This study focuses on the phylogenetic relationships among seven species within the genus Parapenaeupsis, the population genetic variation of Parapenaeupsis sculptilis along Bangladesh coastline of the Bay of Bengal and the phylogeography of P. sculptilis in the Indian Ocean region by analysing cytochrome oxidase subunit 1 barcode (CO1) sequence. No population structure was detected in P. sculptilis collected from two sampling sites along the Bangladesh coastline (AMOVA and Φ ST = ‑0.014, p > 0.05; F ST = 0.061, p = 0.04), which expanded first around 73 (CI: 36‑119) kyr ago. The genealogical relationships in Bangladesh P. sculptilis population are shallow with haplotype diversity (h) of 0.58 and nucleotide diversity (π) of 0.0014. The different P. sculptilis samples from Bangladesh, India and Mozambique of the Indian Ocean revealed connectivity between western Indian Ocean and the Bay of Bengal. The phylogeny within the genus Parapenaeupsis showed a polyphyletic relationships for P. hardickwii and its taxonomy needs to be reevaluated. The study will help for genetic upgradation in aquaculture and monitoring of the population genetic diversity of P. sculptilis

Chironomidae fauna of springs in Iceland: Assessing the ecological relevance behind Tuxen’s spring classification

In 1937, S.L. Tuxen studied the animal community of hot springs in Iceland, and classified springs according to their relative temperature into cold, tepid, and hot. Eighty years after Tuxen’s study, we revisited some of the hot springs in Skagafjörður, Northern Iceland. Our aim was to compare the invertebrate community of 1937 and today, and to assess the stability of hot spring habitats over the years. To test Tuxen’s spring classification on an ecological basis, we furthermore collected chironomid larvae from 24 springs of a broad range of temperature, with samples taken both at the surface area of the spring and at the groundwater level. The chironomid species composition of hot springs differed from that of cold and tepid springs. Whereas Cricotopus sylvestris, Arctopelopia sp., and Procladius sp. characterised the chironomid community in Icelandic hot springs, cold and tepid springs were dominated by Eukiefferiella minor, Orthocladius frigidus and Diamesa spp. Community composition analyses and the exclusive occurrence of taxa in one of the temperature classes validated the ecological relevance of Tuxen’s spring classification for the chironomid species community. Both environmental parameters and invertebrate community of Icelandic hot springs seem to be the same as 80 years ago. Although springs have the potential to provide stable habitats, they are currently under high anthropogenic pressure, and should be increasingly considered in nature conservation.

A complex speciation-richness relationship in a simple neutral model

Speciation is the "elephant in the room" of community ecology. As the ultimate source of biodiversity, its integration in ecology's theoretical corpus is necessary to understand community assembly. Yet, speciation is often completely ignored or stripped of its spatial dimension. Recent approaches based on network theory have allowed ecologists to effectively model complex landscapes. In this study, we use this framework to model allopatric and parapatric speciation in networks of communities and focus on the relationship between speciation, richness, and the spatial structure of communities. We find a strong opposition between speciation and local richness, with speciation being more common in isolated communities and local richness being higher in more connected communities. Unlike previous models, we also find a transition to a positive relationship between speciation and local richness when dispersal is low and the number of communities is small. Also, we use several measures of centrality to characterize the effect of network structure on diversity. The degree, the simplest measure of centrality, is found to be the best predictor of local richness and speciation, although it loses some of its predictive power as connectivity grows. Our framework shows how a simple neutral model can be combined with network theory to reveal complex relationships between speciation, richness, and the spatial organization of populations.Comment: 9 pages, 5 figures, 1 table, 50 reference

Effects of overhead power-lines on the density of groundnesting birds in open sub-arctic habitats

Yearly electricity production has increased steadily in the world in recent decades and the associated overhead power lines are widespread and occur across urban and natural habitats, and often in remote areas where there is little other anthropogenic influence. Here we assessed the effects of overhead power lines on the density of ground-nesting birds in the Icelandic lowlands which host several populations of international importance. The combined breeding density of the eight study species increased significantly from ~112 birds/km2 close (< 50 m) to the power lines to ~177 birds/km2 away (450-500 m) from the power lines, with two of these species (Eurasian Whimbrel Numenius phaeopus and Common Redshank Tringa totanus) increasing significantly with distance from power lines and six species (European Golden Plover Pluvialis apricaria, Common Snipe Gallinago gallinago, Meadow Pipit Anthus pratensis, Black-tailed Godwit Limosa limosa, Dunlin Calidris alpina and Redwing Turdus iliacus) showing no changes. These findings suggest that power lines can influence the breeding density of ground-nesting bird species in their vicinity and that accounting for such effects when planning future infrastructure will be imperative

Subarctic afforestation: Effects of forest plantations on ground-nesting birds in lowland Iceland

Planting forests is a commonly suggested measure to mitigate climate change. The resulting changes in habitat structure can greatly influence the diversity and abundance of pre-existing wildlife. Understanding these consequences is key for avoiding unintended impacts of afforestation on habitats and populations of conservation concern. Afforestation in lowland Iceland has been gaining momentum in recent years and further increases are planned. Iceland supports internationally important breeding populations of several ground-nesting, migratory bird species that mostly breed in open habitats. If afforestation impacts the distribution and abundance of these species, the consequences may be apparent throughout their non-breeding ranges across Europe and Africa. To quantify the effects of plantation forests on the abundance and distribution of ground-nesting birds (in particular waders, Charadriiformes), surveys were conducted on 161 transects (surrounding 118 plantations) perpendicular to forest edges throughout Iceland. The resulting variation in density with distance from plantation was used to estimate the likely changes in bird numbers resulting from future afforestation plans, and to explore the potential effects of different planting configuration (size and number of forest patches) scenarios. Of seven wader species, densities of five (golden plover Pluvialis apricaria, whimbrel Numenius phaeopus, oystercatcher Haematopus ostralegus, dunlin Calidris alpina and black-tailed godwit Limosa limosa) in the 200 m surrounding plantations were just under half of those further away (up to 700 m). Redshank Tringa totanus densities were lowest ≤150 m from the plantation edge while snipe Gallinago gallinago densities were 50% higher close to plantations (0–50 m) than further away (51–700 m), and no consistent effects of plantation height, diameter, density or type were identified. Plantations are typically small and widespread, and simulated scenarios indicated that total declines in bird abundance resulting from planting trees in one large block (1,000 ha) could result in only ~11% of the declines predicted from planting multiple small blocks (1 ha) in similar habitats. Synthesis and application. Planting forests in open landscapes can have severe impacts on populations of ground-nesting birds, which emphasizes the need for strategic planning of tree-planting schemes. Given Iceland's statutory commitments to species protection and the huge contribution of Iceland to global migratory bird flyways, these are challenges that must be addressed quickly, before population-level impacts are observed across migratory ranges

Seasonal variation in the invertebrate community and diet of a top fish predator in a thermally stable spring

Many life-history events in aquatic invertebrates are triggered by seasonal changes in water temperature, but other ecological factors may be important as well. To rule out the confounding effects of changing water temperature, we studied the seasonal dynamics of an aquatic invertebrate community and their effect on a top fish predator in a thermally stable freshwater spring in South Iceland. We sampled benthic invertebrates five times over a year and conducted a mark-recapture study on the top predator in the system, small benthic Arctic charr, Salvelinus alpinus (L.). We assessed variation in diet composition and feeding preferences by calculating the electivity and individual specialisation of each fish at each sampling time. There was a clear separation of winter and summer communities for the benthic invertebrates. The variation in prey availability was also reflected in the fish diet, with higher feeding selectivity in summer than in winter for the highly abundant Chironomidae larvae. In contrast, individual specialisation as a measure of intrapopulation niche variation was higher in winter when prey availability was lower. We furthermore found that groundwater amphipods might play an important role in the winter diet of spring-dwelling Arctic charr. In conclusion, seasonal variation in the invertebrate community is an important factor to consider and has the potential to alter the phenotype (e.g. growth rates) and behaviour (e.g. feeding preferences) of higher trophic levels

Holocene deglaciation drove rapid genetic diversification of Atlantic walrus

Rapid global warming is severely impacting Arctic ecosystems and is predicted to transform the abundance, distribution and genetic diversity of Arctic species, though these linkages are poorly understood. We address this gap in knowledge using palaeogenomics to examine how earlier periods of global warming influenced the genetic diversity of Atlantic walrus (Odobenus rosmarus rosmarus), a species closely associated with sea ice and shallow-water habitats. We analysed 82 ancient and historical Atlantic walrus mitochondrial genomes (mitogenomes), including now-extinct populations in Iceland and the Canadian Maritimes, to reconstruct the Atlantic walrus' response to Arctic deglaciation. Our results demonstrate that the phylogeography and genetic diversity of Atlantic walrus populations was initially shaped by the last glacial maximum (LGM), surviving in distinct glacial refugia, and subsequently expanding rapidly in multiple migration waves during the late Pleistocene and early Holocene. The timing of diversification and establishment of distinct populations corresponds closely with the chronology of the glacial retreat, pointing to a strong link between walrus phylogeography and sea ice. Our results indicate that accelerated ice loss in the modern Arctic may trigger further dispersal events, likely increasing the connectivity of northern stocks while isolating more southerly stocks putatively caught in small pockets of suitable habitat

Monitoring of species’ genetic diversity in Europe varies greatly and overlooks potential climate change impacts

Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. However, genetic diversity has been largely neglected in biodiversity monitoring, and when addressed, it is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. We report an accounting of efforts to monitor population genetic diversity in Europe (genetic monitoring effort, GME), the evaluation of which can help guide future capacity building and collaboration towards areas most in need of expanded monitoring. Overlaying GME with areas where the ranges of selected species of conservation interest approach current and future climate niche limits helps identify whether GME coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area, financial resources and conservation policy influence GME, high values of which only partially match species’ joint patterns of limits to suitable climatic conditions. Populations at trailing climatic niche margins probably hold genetic diversity that is important for adaptation to changing climate. Our results illuminate the need in Europe for expanded investment in genetic monitoring across climate gradients occupied by focal species, a need arguably greatest in southeastern European countries. This need could be met in part by expanding the European Union’s Birds and Habitats Directives to fully address the conservation and monitoring of genetic diversity

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

Mitochondrial DNA variation and population genetic structure of white shrimp

The white shrimp (Fenneropenaeus indicus) is an ecologically and economically important penaeid species, widely distributed in the Indo-Pacific region. To obtain information on the genetic variation and population structure of F. indicus, sequencing analysis was conducted on a fragment of cytochrome oxidase subunit I (COI) of the mitochondrial DNA. Individuals (n = 217) from eight locations covering four main geographic regions along the coastal belt of Sri Lanka were analysed. The sequences, a 602-base pairs (bp) fragment in length, revealed high haplotype and nucleotide diversity that yielded 82 haplotypes. A mismatch analysis produced a unimodal distribution of pairwise differences between haplotypes, consistent with a historic rapid population expansion. Little or no genetic differentiation was observed between most samples, although genetic distances based on pairwise differences between haplotypes started to increase when geographic distances exceeded about 130 km. A population in Bundala (southeast) had lower diversity and was genetically differentiated from the others. This information could be important for the sustainable management and utilization of this resource