scholarly journals Continental-scale patterns of hyper-cryptic diversity within the freshwater model taxon Gammarus fossarum (Crustacea, Amphipoda)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Remi Wattier ◽  
Tomasz Mamos ◽  
Denis Copilaş-Ciocianu ◽  
Mišel Jelić ◽  
Anthony Ollivier ◽  
...  
Keyword(s):  
Evolutionary Ecology ◽  
Taxonomic Status ◽  
Model Organisms ◽  
Cryptic Diversity ◽  
Gammarus Fossarum ◽  
Continental Scale ◽  
Operational Taxonomic Units ◽  
Freshwater Crustacean ◽  
High Level ◽  
Insight Into

Abstract Traditional morphological diagnoses of taxonomic status remain widely used while an increasing number of studies show that one morphospecies might hide cryptic diversity, i.e. lineages with unexpectedly high molecular divergence. This hidden diversity can reach even tens of lineages, i.e. hyper cryptic diversity. Even well-studied model-organisms may exhibit overlooked cryptic diversity. Such is the case of the freshwater crustacean amphipod model taxon Gammarus fossarum. It is extensively used in both applied and basic types of research, including biodiversity assessments, ecotoxicology and evolutionary ecology. Based on COI barcodes of 4926 individuals from 498 sampling sites in 19 European countries, the present paper shows (1) hyper cryptic diversity, ranging from 84 to 152 Molecular Operational Taxonomic Units, (2) ancient diversification starting already 26 Mya in the Oligocene, and (3) high level of lineage syntopy. Even if hyper cryptic diversity was already documented in G. fossarum, the present study increases its extent fourfold, providing a first continental-scale insight into its geographical distribution and establishes several diversification hotspots, notably south-eastern and central Europe. The challenges of recording hyper cryptic diversity in the future are also discussed.

scholarly journals Neogene paleogeography provides context for understanding the origin and spatial distribution of cryptic diversity in a widespread Balkan freshwater amphipod

2017 ◽  
Author(s):  
Michał Grabowski ◽  
Tomasz Mamos ◽  
Karolina Bącela-Spychalska ◽  
Tomasz Rewicz ◽  
Remi A Wattier
Keyword(s):  
Evolutionary History ◽  
28S Rdna ◽  
Cryptic Diversity ◽  
The Balkans ◽  
Operational Taxonomic Units ◽  
Freshwater Biota ◽  
History Of ◽  
Riverine Habitats ◽  
Coi Sequences ◽  
High Level

Background. The Balkans are a major biodiversity and endemism hotspot, worldwide. Among the freshwater biota, amphipods are known for their high cryptic diversity. However, little is known about the temporal and paleogeographic aspects of their evolutionary history. We used paleogeography as a framework for understanding the onset of diversification in Gammarus roeselii: 1) we hypothesised that, given the high number of isolated waterbodies in the Balkans, the species is characterised by high level of cryptic diversity, even on a local scale; 2) the long geological history of the region might promote pre-Pleistocene divergence between lineages; 3) given that G. roeselii thrives both in lakes and rivers, its evolutionary history could be linked to the Balkan Neogene paleolake system; 4) we inspected whether the Pleistocene decline of hydrological networks could have any impact on the diversification of G. roeselii. Material and Methods. DNA was extracted from 136 individuals collected from 26 sites all over Balkans. All individuals were amplified for ca. 650 bp long fragment of the mtDNA cytochrome oxidase subunit I (COI). After defining molecular operational taxonomic units (MOTU) based on COI, 50 individuals were amplified for ca. 900 bp long fragment of the nuclear 28S rDNA. Molecular diversity, divergence, differentiation and historical demography based on COI sequences were estimated for each MOTU. The relative frequency, geographic distribution and molecular divergence between COI haplotypes were presented as a median-joining network. COI was used also to reconstruct time-calibrated phylogeny with Bayesian inference. Probabilities of ancestors' occurrence in riverine or lacustrine habitats, as well their possible geographic locations, were estimated with the Bayesian method. A Neighbour Joining tree was constructed to illustrate the phylogenetic relationships between 28S rDNA haplotypes. Results. We revealed that G. roeselii includes at least 13 cryptic species or molecular operational taxonomic units (MOTUs), mostly of Miocene origin. A substantial Pleistocene diversification within-MOTUs was observed in several cases. We evidenced secondary contacts between very divergent MOTUs and introgression of nDNA. The Miocene ancestors could live in either lacustrine or riverine habitats yet their presumed geographic localisations overlapped with those of the Neogene lakes. Several extant riverine populations had Pleistocene lacustrine ancestors. Discussion. Neogene divergence of lineages resulting in substantial cryptic diversity may be a common phenomenon in extant freshwater benthic crustaceans occupying areas that were not glaciated during the Pleistocene. Evolution of G. roeselii could be associated with gradual deterioration of the paleolakes. The within-MOTU diversification might be driven by fragmentation of river systems during the Pleistocene. Extant ancient lakes could serve as local microrefugia during that time.

scholarly journals Neogene paleogeography provides context for understanding the origin and spatial distribution of cryptic diversity in a widespread Balkan freshwater amphipod

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3016 ◽  
Author(s):  
Michał Grabowski ◽  
Tomasz Mamos ◽  
Karolina Bącela-Spychalska ◽  
Tomasz Rewicz ◽  
Remi A. Wattier
Keyword(s):  
Evolutionary History ◽  
28S Rdna ◽  
Cryptic Diversity ◽  
The Balkans ◽  
Operational Taxonomic Units ◽  
Freshwater Biota ◽  
History Of ◽  
Riverine Habitats ◽  
Coi Sequences ◽  
High Level

BackgroundThe Balkans are a major biodiversity and endemism hotspot, worldwide. Among the freshwater biota, amphipods are known for their high cryptic diversity. However, little is known about the temporal and paleogeographic aspects of their evolutionary history. We used paleogeography as a framework for understanding the onset of diversification inGammarus roeselii: (1) we hypothesised that, given the high number of isolated waterbodies in the Balkans, the species is characterised by high level of cryptic diversity, even on a local scale; (2) the long geological history of the region might promote pre-Pleistocene divergence between lineages; (3) given thatG. roeseliithrives both in lakes and rivers, its evolutionary history could be linked to the Balkan Neogene paleolake system; (4) we inspected whether the Pleistocene decline of hydrological networks could have any impact on the diversification ofG. roeselii.Material and MethodsDNA was extracted from 177 individuals collected from 26 sites all over Balkans. All individuals were amplified for ca. 650 bp long fragment of the mtDNA cytochrome oxidase subunit I (COI). After defining molecular operational taxonomic units (MOTU) based on COI, 50 individuals were amplified for ca. 900 bp long fragment of the nuclear 28S rDNA. Molecular diversity, divergence, differentiation and historical demography based on COI sequences were estimated for each MOTU. The relative frequency, geographic distribution and molecular divergence between COI haplotypes were presented as a median-joining network. COI was used also to reconstruct time-calibrated phylogeny with Bayesian inference. Probabilities of ancestors’ occurrence in riverine or lacustrine habitats, as well their possible geographic locations, were estimated with the Bayesian method. A Neighbour Joining tree was constructed to illustrate the phylogenetic relationships between 28S rDNA haplotypes.ResultsWe revealed thatG. roeseliiincludes at least 13 cryptic species or molecular operational taxonomic units (MOTUs), mostly of Miocene origin. A substantial Pleistocene diversification within-MOTUs was observed in several cases. We evidenced secondary contacts between very divergent MOTUs and introgression of nDNA. The Miocene ancestors could live in either lacustrine or riverine habitats yet their presumed geographic localisations overlapped with those of the Neogene lakes. Several extant riverine populations had Pleistocene lacustrine ancestors.DiscussionNeogene divergence of lineages resulting in substantial cryptic diversity may be a common phenomenon in extant freshwater benthic crustaceans occupying areas that were not glaciated during the Pleistocene. Evolution ofG. roeseliicould be associated with gradual deterioration of the paleolakes. The within-MOTU diversification might be driven by fragmentation of river systems during the Pleistocene. Extant ancient lakes could serve as local microrefugia during that time.

scholarly journals Neogene paleogeography provides context for understanding the origin and spatial distribution of cryptic diversity in a widespread Balkan freshwater amphipod

2017 ◽  
Author(s):  
Michał Grabowski ◽  
Tomasz Mamos ◽  
Karolina Bącela-Spychalska ◽  
Tomasz Rewicz ◽  
Remi A Wattier
Keyword(s):  
Evolutionary History ◽  
28S Rdna ◽  
Cryptic Diversity ◽  
The Balkans ◽  
Operational Taxonomic Units ◽  
Freshwater Biota ◽  
History Of ◽  
Riverine Habitats ◽  
Coi Sequences ◽  
High Level

Background. The Balkans are a major biodiversity and endemism hotspot, worldwide. Among the freshwater biota, amphipods are known for their high cryptic diversity. However, little is known about the temporal and paleogeographic aspects of their evolutionary history. We used paleogeography as a framework for understanding the onset of diversification in Gammarus roeselii: 1) we hypothesised that, given the high number of isolated waterbodies in the Balkans, the species is characterised by high level of cryptic diversity, even on a local scale; 2) the long geological history of the region might promote pre-Pleistocene divergence between lineages; 3) given that G. roeselii thrives both in lakes and rivers, its evolutionary history could be linked to the Balkan Neogene paleolake system; 4) we inspected whether the Pleistocene decline of hydrological networks could have any impact on the diversification of G. roeselii. Material and Methods. DNA was extracted from 136 individuals collected from 26 sites all over Balkans. All individuals were amplified for ca. 650 bp long fragment of the mtDNA cytochrome oxidase subunit I (COI). After defining molecular operational taxonomic units (MOTU) based on COI, 50 individuals were amplified for ca. 900 bp long fragment of the nuclear 28S rDNA. Molecular diversity, divergence, differentiation and historical demography based on COI sequences were estimated for each MOTU. The relative frequency, geographic distribution and molecular divergence between COI haplotypes were presented as a median-joining network. COI was used also to reconstruct time-calibrated phylogeny with Bayesian inference. Probabilities of ancestors' occurrence in riverine or lacustrine habitats, as well their possible geographic locations, were estimated with the Bayesian method. A Neighbour Joining tree was constructed to illustrate the phylogenetic relationships between 28S rDNA haplotypes. Results. We revealed that G. roeselii includes at least 13 cryptic species or molecular operational taxonomic units (MOTUs), mostly of Miocene origin. A substantial Pleistocene diversification within-MOTUs was observed in several cases. We evidenced secondary contacts between very divergent MOTUs and introgression of nDNA. The Miocene ancestors could live in either lacustrine or riverine habitats yet their presumed geographic localisations overlapped with those of the Neogene lakes. Several extant riverine populations had Pleistocene lacustrine ancestors. Discussion. Neogene divergence of lineages resulting in substantial cryptic diversity may be a common phenomenon in extant freshwater benthic crustaceans occupying areas that were not glaciated during the Pleistocene. Evolution of G. roeselii could be associated with gradual deterioration of the paleolakes. The within-MOTU diversification might be driven by fragmentation of river systems during the Pleistocene. Extant ancient lakes could serve as local microrefugia during that time.

scholarly journals Overview of the Genetic Diversity of African Macrotermes (Termitidae: Macrotermitinae) and Implications for Taxonomy, Ecology and Food Science

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 518
Author(s):  
Bronwyn Egan ◽  
Zwannda Nethavhani ◽  
Barbara van Asch
Keyword(s):  
Negative Impact ◽  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Food Science ◽  
Cryptic Diversity ◽  
African Species ◽  
Genetic Groups ◽  
Wide Range ◽  
Coi Sequences ◽  
High Level

Macrotermes termites play important ecological roles and are consumed by many communities as a delicacy and dietary complement throughout Africa. However, lack of reliable morphological characters has hampered studies of Macrotermes diversity in a wide range of scientific fields including ecology, phylogenetics and food science. In order to place our preliminary assessment of the diversity of Macrotermes in South Africa in context, we analysed a comprehensive dataset of COI sequences for African species including new and publicly available data. Phylogenetic reconstruction and estimates of genetic divergence showed a high level of incongruity between species names and genetic groups, as well as several instances of cryptic diversity. We identified three main clades and 17 genetic groups in the dataset. We propose that this structure be used as a background for future surveys of Macrotermes diversity in Africa, thus mitigating the negative impact of the present taxonomic uncertainties in the genus. The new specimens collected in Limpopo fell into four distinct genetic groups, suggesting that the region harbours remarkable Macrotermes diversity relative to other African regions surveyed in previous studies. This work shows that African Macrotermes have been understudied across the continent, and that the genus contains cryptic diversity undetectable by classic taxonomy. Furthermore, these results may inform future taxonomic revisions in Macrotermes, thus contributing to advances in termitology.

Insight into the formation of a continuous sheath structure for the PS phase in tri-continuous PVDF/PS/HDPE blends

RSC Advances ◽  
2016 ◽  
Vol 6 (1) ◽  
pp. 439-447 ◽  
Author(s):  
Rui Dou ◽  
Shuanglin Li ◽  
Yan Shao ◽  
Bo Yin ◽  
Mingbo Yang
Keyword(s):  
Ternary Blends ◽  
Continuous Structure ◽  
High Level ◽  
Very High ◽  
Insight Into ◽  
Sheath Structure

A hierarchical tri-continuous structure is formed and controlled in PVDF/PS/HDPE ternary blends. A very high level of PS continuity, about 80%, is achieved only with a PS volume composition as low as 11 vol%.

scholarly journals Transgenic Epigenetics: Using Transgenic Organisms to Examine Epigenetic Phenomena

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Lori A. McEachern
Keyword(s):  
Molecular Mechanisms ◽  
Model Organism ◽  
Evolutionary Conservation ◽  
Model Organisms ◽  
Valuable Insight ◽  
Epigenetic Control ◽  
Transgenic Organisms ◽  
Epigenetic Analysis ◽  
Insight Into ◽  
Epigenetic Processes

Non-model organisms are generally more difficult and/or time consuming to work with than model organisms. In addition, epigenetic analysis of model organisms is facilitated by well-established protocols, and commercially-available reagents and kits that may not be available for, or previously tested on, non-model organisms. Given the evolutionary conservation and widespread nature of many epigenetic mechanisms, a powerful method to analyze epigenetic phenomena from non-model organisms would be to use transgenic model organisms containing an epigenetic region of interest from the non-model. Interestingly, while transgenic Drosophila and mice have provided significant insight into the molecular mechanisms and evolutionary conservation of the epigenetic processes that target epigenetic control regions in other model organisms, this method has so far been under-exploited for non-model organism epigenetic analysis. This paper details several experiments that have examined the epigenetic processes of genomic imprinting and paramutation, by transferring an epigenetic control region from one model organism to another. These cross-species experiments demonstrate that valuable insight into both the molecular mechanisms and evolutionary conservation of epigenetic processes may be obtained via transgenic experiments, which can then be used to guide further investigations and experiments in the species of interest.

scholarly journals Reconstructing feedback representations in ventral visual pathway with a generative adversarial autoencoder

2020 ◽  
Author(s):  
Haider Al-Tahan ◽  
Yalda Mohsenzadeh
Keyword(s):  
Neural Network ◽  
Visual Information ◽  
Visual Pathway ◽  
Functional Magnetic Resonance ◽  
Low Level ◽  
Ventral Visual Pathway ◽  
High Level ◽  
Feedback Connections ◽  
The Brain ◽  
Insight Into

AbstractWhile vision evokes a dense network of feedforward and feedback neural processes in the brain, visual processes are primarily modeled with feedforward hierarchical neural networks, leaving the computational role of feedback processes poorly understood. Here, we developed a generative autoencoder neural network model and adversarially trained it on a categorically diverse data set of images. We hypothesized that the feedback processes in the ventral visual pathway can be represented by reconstruction of the visual information performed by the generative model. We compared representational similarity of the activity patterns in the proposed model with temporal (magnetoencephalography) and spatial (functional magnetic resonance imaging) visual brain responses. The proposed generative model identified two segregated neural dynamics in the visual brain. A temporal hierarchy of processes transforming low level visual information into high level semantics in the feedforward sweep, and a temporally later dynamics of inverse processes reconstructing low level visual information from a high level latent representation in the feedback sweep. Our results append to previous studies on neural feedback processes by presenting a new insight into the algorithmic function and the information carried by the feedback processes in the ventral visual pathway.Author summaryIt has been shown that the ventral visual cortex consists of a dense network of regions with feedforward and feedback connections. The feedforward path processes visual inputs along a hierarchy of cortical areas that starts in early visual cortex (an area tuned to low level features e.g. edges/corners) and ends in inferior temporal cortex (an area that responds to higher level categorical contents e.g. faces/objects). Alternatively, the feedback connections modulate neuronal responses in this hierarchy by broadcasting information from higher to lower areas. In recent years, deep neural network models which are trained on object recognition tasks achieved human-level performance and showed similar activation patterns to the visual brain. In this work, we developed a generative neural network model that consists of encoding and decoding sub-networks. By comparing this computational model with the human brain temporal (magnetoencephalography) and spatial (functional magnetic resonance imaging) response patterns, we found that the encoder processes resemble the brain feedforward processing dynamics and the decoder shares similarity with the brain feedback processing dynamics. These results provide an algorithmic insight into the spatiotemporal dynamics of feedforward and feedback processes in biological vision.

scholarly journals Exploring citizen science in post-socialist space: Uncovering its hidden character in the Czech Republic

2019 ◽  
Vol 27 (4) ◽  
pp. 241-253 ◽  
Author(s):  
Barbora Duží ◽  
Robert Osman ◽  
Jiří Lehejček ◽  
Eva Nováková ◽  
Pavel Taraba ◽  
...  
Keyword(s):  
Czech Republic ◽  
Citizen Science ◽  
The Czech Republic ◽  
The Public ◽  
Public Representation ◽  
Science Projects ◽  
Definition Of ◽  
High Level ◽  
Search Approach ◽  
Insight Into

Abstract Citizen science is a relatively new phenomenon in the Czech Republic and currently a general overview of existing citizen science projects is not available. This presents the challenge to uncover the ‘hidden’ citizen science landscapes. The main objective of this paper is to explore the (public) representation of citizen science (CS) projects and to describe their heterogeneity. The study aims to answer the question of what type of projects in the Czech Republic meet the definition of citizen science. Based on a specific methodological data-base search approach, we compiled a set of CS projects (N = 73). During the classification process, two general citizen science categories were identified. The first group (N = 46) consists of “pure” CS projects with a prevalence towards the natural sciences, principally ornithology, and thus corresponding to general European trends. Citizens usually participate in such research in the form of data collection and basic interpretation, and a high level of cooperation between academia and NGOs was detected. The second group of “potential” CS projects (N = 27) entails various forms of public participation in general, frequently coordinated by NGOs. Based on these results, we discuss the position of citizen science in the Czech Republic, including socially-oriented citizen science. Further research is strongly encouraged to achieve a more in-depth insight into this social phenomenon.

The enigmatic groundwater amphipod Awacaris kawasawai revisited: synonymisation of the genus Sternomoera, with molecular phylogenetic analyses of Awacaris and Sternomoera species (Crustacea : Amphipoda : Pontogeneiidae)

2017 ◽  
Vol 31 (2) ◽  
pp. 125 ◽  
Author(s):  
Ko Tomikawa ◽  
Masaki Kyono ◽  
Keiko Kuribayashi ◽  
Takafumi Nakano
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
28S Rrna ◽  
Ancestral State ◽  
Cryptic Diversity ◽  
Japanese Archipelago ◽  
Molecular Phylogenetic ◽  
The Japanese Archipelago ◽  
Kochi Prefecture

Amphipod crustaceans are dominant in subterranean habitats, and members of eight genera are endemic to groundwater environments in the Japanese Archipelago. The taxonomic status of two of these genera remains unclear, because their original descriptions were incomplete. The descriptions of the enigmatic subterranean monotypic genus Awacaris and its type species, A. kawasawai Uéno, 1971, are revisited here. Awacaris kawasawai was originally described based on specimens from a subterranean stream at Himise Cave, Tokushima Prefecture, Shikoku, Japan. Recently, a new population of A. kawasawai was found at Saruta Cave, Kochi Prefecture, Shikoku. Detailed observation of the newly collected specimens reveals the presence of sternal gills, which is the diagnostic character of the pontogeneiid genus Sternomoera, making the validity of Sternomoera open to question. Phylogenetic analyses using nuclear 28S rRNA and mitochondrial cytochrome c oxidase subunit I markers demonstrate that A. kawasawai forms a well-supported clade with the subterranean S. morinoi Tomikawa and Ishimaru, 2014. In addition, phylogenetic analysis reveals cryptic diversity in epigean species of Sternomoera. Ancestral state reconstruction suggests that catadromous Sternomoera species have evolved from freshwater ancestors. Based on our morphological and phylogenetic analysis of Awacaris and Sternomoera species, it is concluded here that Sternomoera should be treated as a subjective junior synonym of Awacaris.

Sign in / Sign up

Export Citation Format

Share Document