scholarly journals Community assembly and metaphylogeography of soil biodiversity: insights from haplotype-level community DNA metabarcoding within an oceanic island

2022 ◽  
Author(s):  
Carmelo Andujar ◽  
Paula Arribas ◽  
Heriberto López ◽  
Yurena Arjona ◽  
Antonio Pérez-Delgado ◽  
...  
Keyword(s):  
Community Assembly ◽  
Sequence Data ◽  
Spatial Scales ◽  
Oceanic Island ◽  
Soil Mesofauna ◽  
Soil Biodiversity ◽  
Dna Sequence Data ◽  
Dna Metabarcoding ◽  
Patterns And Processes

Most of our understanding of island diversity comes from the study of aboveground systems, while the patterns and processes of diversification and community assembly for belowground biotas remain poorly understood. Here we take advantage of a relatively young and dynamic oceanic island to advance our understanding of eco-evolutionary processes driving community assembly within soil mesofauna. Using whole organism community DNA (wocDNA) metabarcoding and the recently developed metaMATE pipeline, we have generated spatially explicit and reliable haplotype-level DNA sequence data for soil mesofaunal assemblages sampled across the four main habitats within the island of Tenerife. Community ecological and metaphylogeographic analyses have been performed at multiple levels of genetic similarity, from haplotypes to species and supraspecific groupings. Broadly consistent patterns of local-scale species richness across different insular habitats have been found, whereas local insular richness is lower than in continental settings. Our results reveal an important role for niche conservatism as a driver of insular community assembly of soil mesofauna, with only limited evidence for habitat shifts promoting diversification. Furthermore, support is found for a fundamental role of habitat in the assembly of soil mesofauna, where habitat specialism is mainly due to colonisation and the establishment of preadapted species. Hierarchical patterns of distance decay at the community level and metaphylogeographical analyses support a pattern of geographic structuring over limited spatial scales, from the level of haplotypes through to species and lineages, as expected for taxa with strong dispersal limitations. Our results demonstrate the potential for wocDNA metabarcoding to advance our understanding of biodiversity.

scholarly journals Phylogeography of two Andean frogs: Test of vicariance versus elevational gradient models of diversification

2019 ◽  
Author(s):  
Daria Koscinski ◽  
Paul Handford ◽  
Pablo L. Tubaro ◽  
Peiwen Li ◽  
Stephen C. Lougheed
Keyword(s):  
Sequence Data ◽  
Environmental Gradients ◽  
Spatial Scales ◽  
Elevational Gradient ◽  
Northwestern Argentina ◽  
Dna Sequence Data ◽  
The Andes ◽  
Common Causes ◽  
History Of ◽  
Historical Range

ABSTRACTThe tropical and subtropical Andes have among the highest levels of biodiversity in the world. Understanding the forces that underlie speciation and diversification in the Andes is a major focus of research. Here we tested two hypotheses of species origins in the Andes: 1. Vicariance mediated by orogenesis or shifting habitat distribution. 2. Parapatric diversification along elevational environmental gradients. We also sought insights on the factors that impacted the phylogeography of co-distributed taxa, and the influences of divergent species ecology on population genetic structure. We used phylogeographic and coalescent analyses of nuclear and mitochondrial DNA sequence data to compare genetic diversity and evolutionary history of two frog species: Pleurodema borellii (Family: Leiuperidae, 130 individuals; 20 sites), and Hypsiboas riojanus (Family: Hyllidae, 258 individuals; 23 sites) across their shared range in northwestern Argentina. The two showed concordant phylogeographic structuring, and our analyses support the vicariance model over the elevational gradient model. However, Pleurodema borellii exhibited markedly deeper temporal divergence (≥4 Ma) than H. riojanus (1-2 Ma). The three main mtDNA lineages of P. borellii were nearly allopatric and diverged between 4-10 Ma. At similar spatial scales, differentiation was less in the putatively more habitat-specialized H. riojanus than in the more generalist P. borellii. Similar allopatric distributions of major lineages for both species implies common causes of historical range fragmentation and vicariance. However, different divergence times among clades presumably reflect different demographic histories, permeability of different historical barriers at different times, and/or difference in life history attributes and sensitivities to historical environmental change. Our research enriches our understanding of the phylogeography of the Andes in northwestern Argentina.

scholarly journals Linking Patterns and Processes of Tree Community Assembly Across Spatial Scales in Tropical Montane Forests

2020 ◽  
Vol 101 (3) ◽  
Author(s):  
Guillermo Bañares‐de‐Dios ◽  
Manuel J. Macía ◽  
Íñigo Granzow‐de la Cerda ◽  
Itziar Arnelas ◽  
Gabriel Martins Carvalho ◽  
...  
Keyword(s):  
Community Assembly ◽  
Spatial Scales ◽  
Montane Forests ◽  
Tropical Montane Forests ◽  
Tree Community ◽  
Patterns And Processes

Linking patterns and processes of tree community assembly across spatial scales in tropical montane forests

Ecology ◽  
2020 ◽  
Vol 101 (7) ◽  
Author(s):  
Guillermo Bañares‐de‐Dios ◽  
Manuel J. Macía ◽  
Íñigo Granzow‐de la Cerda ◽  
Itziar Arnelas ◽  
Gabriel Martins de Carvalho ◽  
...  
Keyword(s):  
Community Assembly ◽  
Spatial Scales ◽  
Montane Forests ◽  
Tropical Montane Forests ◽  
Tree Community ◽  
Patterns And Processes

scholarly journals Assessment of species gaps in DNA barcode libraries of non-indigenous species (NIS) occurring in European coastal regions

2020 ◽  
Vol 4 ◽  
Author(s):  
Sofia Duarte ◽  
Pedro E. Vieira ◽  
Filipe O. Costa
Keyword(s):  
Sequence Data ◽  
Dna Barcode ◽  
Indigenous Species ◽  
Coastal Environments ◽  
Taxonomic Assignment ◽  
Dna Sequence Data ◽  
Marker Data ◽  
Dna Metabarcoding ◽  
Assessment Techniques ◽  
Non Indigenous Species

DNA metabarcoding has the capacity to bolster current biodiversity assessment techniques, including the early detection and monitoring of non-indigenous species (NIS). However, the success of this approach is greatly dependent on the availability, taxonomic coverage and reliability of reference sequences in genetic databases, whose deficiencies can potentially compromise species identifications at the taxonomic assignment step. In this study we assessed lacunae in availability of DNA sequence data from four barcodes (COI, 18S, rbcL and matK) for NIS occurring in European marine and coastal environments. NIS checklists were based on EASIN and AquaNIS databases. The highest coverage was found for COI for Animalia and rbcL for Plantae (up to 63%, for both) and 18S for Chromista (up to 51%), that greatly increased when only high impact species were taken into account (up to 82 to 89%). Results show that different markers have unbalanced representations in genetic databases, implying that the parallel use of more than one marker can act complimentarily and may greatly increase NIS identification rates through DNA-based tools. Furthermore, based on the COI marker, data for approximately 30% of the species had maximum intra-specific distances higher than 3%, suggesting that many NIS may have undescribed or cryptic diversity. Although completing the gaps in reference libraries is essential to make the most of the potential of the DNA-based tools, a careful compilation, verification and annotation of available sequences is fundamental to assemble large curated and reliable reference libraries that provide support for rigorous species identifications.

Taxonomy and DNA sequence databases: A perfect match?

2011 ◽  
Vol 4 (3) ◽  
pp. 221-236 ◽  
Author(s):  
John James Wilson
Keyword(s):  
Dna Sequence ◽  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Perfect Match ◽  
Dna Sequence Data ◽  
Online Databases ◽  
Sequence Databases ◽  
Diversity Of Life

AbstractDespite the declining number of traditional taxonomists, our knowledge of Earth's biodiversity continues to grow in the form of DNA sequence data. Freely available through online databases, analyses of sequence datasets are increasingly used as an alternative for the traditional taxonomic process. Species identifications have become “DNA barcoding,” new species discoveries are characterised by genetic divergences, and traditional classification has been supplanted by molecular phylogenetics. These developments are illustrated through a case study investigating the identities of Taygetis butterflies of Costa Rica. Here I review prospects and problems with the molecularization of taxonomy and the key role of publicly available nucleotide sequence databases in efforts to catalogue diversity of life.

scholarly journals Role of the Dominant Species on the Distributions of Neighbor Species in a Subtropical Forest

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 352
Author(s):  
Shiguang Wei ◽  
Lin Li ◽  
Juyu Lian ◽  
Scott E. Nielsen ◽  
Zhigao Wang ◽  
...  
Keyword(s):  
Community Assembly ◽  
Dominant Species ◽  
Scale Effects ◽  
Southern China ◽  
Spatial Scales ◽  
Null Model ◽  
Subtropical Forest ◽  
Successional Stage ◽  
Species Groups

Understanding the role of dominant species in structuring the distribution of neighbor species is an important part of understanding community assembly, a central goal of ecology. Phylogenetic information helps resolve the multitude of processes driving community assembly and the importance of evolution in the assembly process. In this study, we classified species in a 20-ha subtropical forest in southern China into groups with different degrees of phylogenetic relatedness to the dominant species Castanopsis chinensis. Species surrounding individuals of C. chinensis were sampled in an equal area annulus at six spatial scales, counting the percent of relatives and comparing this to permutation tests of a null model and variance among species groups. The results demonstrated that dominant species affected their relatives depending on community successional stage. Theory would predict that competitive exclusion and density-dependence mechanisms should lead to neighbors that are more distant in phylogeny from C. chinensis. However, in mature forests distant relatives were subjected to competitive repulsion by C. chinensis, while environment filtering led to fewer distant species, regardless of scale. A variety of biological and non-biological factors appear to result in a U-shaped quantitative distribution determined by the dominant species C. chinensis. Scale effects also influenced the dominant species. As a dominant species, C. chinensis played an important role in structuring the species distributions and coexistence of neighbor species in a subtropical forest.

scholarly journals Introduction and synthesis: plant phylogeny and the origin of major biomes

2004 ◽  
Vol 359 (1450) ◽  
pp. 1455-1464 ◽  
Author(s):  
R. Toby Pennington ◽  
Quentin C. B. Cronk ◽  
James A. Richardson
Keyword(s):  
Phylogenetic Trees ◽  
Environmental Changes ◽  
Sequence Data ◽  
Long Distance ◽  
Future Studies ◽  
Biogeographic Patterns ◽  
Dna Sequence Data ◽  
History Of ◽  
Time Of Origin

Phylogenetic trees based upon DNA sequence data, when calibrated with a dimension of time, allow inference of: (i) the pattern of accumulation of lineages through time; (ii) the time of origin of monophyletic groups; (iii) when lineages arrived in different geographical areas; (iv) the time of origin of biome–specific morphologies. This gives a powerful new view of the history of biomes that in many cases is not provided by the incomplete plant fossil record. Dated plant phylogenies for angiosperm families such as Leguminoaceae (Fabaceae), Melastomataceae sensu stricto , Annonaceae and Rhamnaceae indicate that long–distance, transoceanic dispersal has played an important role in shaping their distributions, and that this can obscure any effect of tectonic history, previously assumed to have been the major cause of their biogeographic patterns. Dispersal from other continents has also been i mportant in the assembly of the Amazonian rainforest flora and the Australian flora. Comparison of dated biogeographic patterns of plants and animals suggests that recent long–distance dispersal might be more prevalent in plants, which has major implications for community assembly and coevolution. Dated plant phylogenies also reveal the role of past environmental changes on the evolution of lineages in species–rich biomes, and show that recent Plio–Pleistocene diversification has contributed substantially to their current species richness. Because of the critical role of fossils and morphological characters in assigning ages to nodes in phylogenetic trees, future studies must include careful morphological consideration of fossils and their extant relatives in a phylogenetic context. Ideal study systems will be based upon DNA sequence data from multiple loci and multiple fossil calibrations. This allows cross–validation both of age estimates from different loci, and from different fossil calibrations. For a more complete view of biome history, future studies should emphasize full taxon sampling in ecologically important groups, and should focus on geographical areas for which few species–level phylogenies are available, such as tropical Africa and Asia. These studies are urgent because understanding the history of biomes can both inform conservation decisions, and help predict the effects of future environmental changes at a time when biodiversity is being impacted on an unprecedented scale.

scholarly journals High dispersal levels and lake warming are emergent drivers of cyanobacterial community assembly over the Anthropocene in peri-Alpine lakes

2018 ◽  
Author(s):  
Marie-Eve Monchamp ◽  
Piet Spaak ◽  
Francesco Pomati
Keyword(s):  
Stochastic Processes ◽  
Climate Warming ◽  
Community Assembly ◽  
Sequence Data ◽  
Environmental Gradients ◽  
Spatial Scales ◽  
Alpine Lakes ◽  
Cyanobacterial Community ◽  
Water Column Stability ◽  
High Dispersal

Disentangling the relative importance of deterministic and stochastic processes in shaping natural communities is central to ecology. Studies on community assembly over broad temporal and spatial scales in aquatic microorganisms are scarce. Here, we used 16S rDNA sequence data from lake sediments to test for community assembly patterns in cyanobacterial phylogenies across ten European peri-Alpine lakes and over a century of eutrophication and climate warming. We studied phylogenetic similarity in cyanobacterial assemblages over spatial and temporal distance, and environmental gradients, comparing detected patterns with theoretical expectations from deterministic and stochastic processes. We found limited evidence for deviation of lake communities from a random assembly model and no significant effects of geographic distance on phylogenetic similarity, suggesting no dispersal limitation and high levels of stochastic assembly. We did not detect a significant effect of phosphorus and nitrogen levels on deviation of community phylogenies from random. We found however a significant decay of phylogenetic similarity for non-random communities over a gradient of air temperature and water column stability. We show how phylogenetic data from sedimentary archives can improve our understanding of microbial community assembly processes, and support previous evidence that climate warming has been the strongest environmental driver of cyanobacterial community assembly over the Anthropocene.

Biodiversity at the molecular genetic level: experiences from disparate macroorganisms

1994 ◽  
Vol 345 (1311) ◽  
pp. 59-64 ◽  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Sequence Data ◽  
Molecular Genetic ◽  
Dna Sequence Data ◽  
Genetic Level ◽  
Management Policies ◽  
Term Maintenance

Genetic variation is the basis of adaptive flexibility in populations and is the ultimate evolutionary basis of much species and community-level diversity. Accordingly, the preservation and maintenance of genetic diversity has a high priority in many conservation programmes. This paper discusses how genetic diversity is measured at the molecular level, including some newer measures made possible with restriction site or DNA sequence data as well as the development of a phylogenetic approach to assessing the significance of genetic variation within a species. These measures of genetic diversity are then used to re-examine the validity of the 50/500 rule of conservation biology; a rule that states that populations should have no fewer than 50 individuals for short-term maintenance of genetic variation and no fewer than 500 individuals for long-term maintenance. Both the 50 and 500 parts of this rule are found to be invalid and frequently misleading. Instead of invoking ‘universal’ rules, conservation biologists should recognize the role of biodiversity in management policies. Not all species are the same, and we need more research and a willingness to try novel approaches rather than naively apply a ‘rule’ that has no demonstrable generality.

Sign in / Sign up

Export Citation Format

Share Document