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 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.

scholarly journals DNA barcodes combined with geometric morphometry challenge species hypothesis in palaemonid shrimp

2021 ◽  
Vol 4 ◽  
Author(s):  
Aleksandra Jablonska ◽  
Nicolas Navarro ◽  
Remi Laffont ◽  
Remi Wattier ◽  
Vladimir Pesic ◽  
...  
Keyword(s):  
Taxonomic Status ◽  
Balkan Peninsula ◽  
Integrative Approach ◽  
Shape Variation ◽  
Separate Species ◽  
Geometric Morphometric ◽  
The Balkans ◽  
Operational Taxonomic Units ◽  
Freshwater Shrimps ◽  
Coi Sequences

Although the Mediterranean Region is known as a hotspot for biodiversity and endemism its freshwater fauna is still greatly unexplored, and even the emblematic taxa such as decapods require in-depth integrative investigation. In our research we used integrative approach composed of various geometric morphometric and molecular methods to challenge the taxonomic status of two freshwater shrimps representing Palaemonidae: Palaemon antennarius and Palaemon minos. Basing on 352 COI sequences, three Molecular Operational Taxonomic Units (MOTUs) were defined. Two of them belonged to P. antennarius: first inhabiting Apennine Peninsula and Sicily, the second one from the Balkan Peninsula. The third MOTU corresponded to Palaemon minos from Crete. The Balkan MOTU of P. antennarius was closer to P. minos in terms of genetics, than to the other conspecific MOTU. The carapace shape variation, studied on 180 individuals, was mainly explained by the geographic distribution. Balkan and Cretan groups were clearly distinguished, while other samples were distributed along the shape gradient from Sicily and southern Apennine Peninsula to the Balkans. The results of our study showed that, either the MOTU assigned to the Apennine Peninsula and Sicily constitutes a separate species or, alternatively, P. minos should be synonymised with P. antennarius.

scholarly journals Persistence and invasiveness of high-level heteroplasmy through biparental transmission of a selfish mitochondrion in Drosophila

2020 ◽  
Author(s):  
Guilherme C. Baião ◽  
Anton Strunov ◽  
Eleanor Heyworth ◽  
Daniela I. Schneider ◽  
Julia Thoma ◽  
...  
Keyword(s):  
Species Complex ◽  
Evolutionary History ◽  
High Titer ◽  
Genomic Integrity ◽  
Male And Female ◽  
Low Level ◽  
Nuclear Background ◽  
History Of ◽  
High Level ◽  
Drosophila Paulistorum

ABSTRACTHeteroplasmy is the coexistence of more than one type of mitochondria in an organism. Although widespread sequencing has identified several cases of transient or low-level heteroplasmy that primarily occur through mutation or paternal leakage, stable, high-titer heteroplasmy remains rare in animals. In this study we present a unique, stable and high-level heteroplasmy in male and female flies belonging to the neotropical Drosophila paulistorum species complex. We show that mitochondria of D. paulistorum are polyphyletic and form two clades, α and β, with two subclades each. Mitochondria of the α2 subclade appear functional based on their genomic integrity but are exclusively found in heteroplasmic flies and never in homoplasmy, suggesting that they are a secondary mitotype with distinct functionality from the primary mitochondria. Using qPCR, we show that α2 titer do not respond to energetic demands of the cell and are generally higher in males than females. By crossing hetero- and homoplasmic flies, we find that α2 can be transmitted to their offspring via both parents and that levels are dependent on nuclear background. Following α2 mitotype levels during embryogenesis, we demonstrate that this secondary mitotype replicates rapidly just after fertilization of the egg in a period when primary mitochondria are dormant. This so-called “Replication precox” mitochondrial phenotype likely prevents the α2 mitotype from being outcompeted by the primary mitotype – and thereby secures its persistence and further spread as a selfish mitochondrion, we hereby designate “Spartacus”. Finally, we reconstruct the evolutionary history of mitochondria in the willistoni subgroup uncovering signs of multiple mitochondrial losses and introgressions. Our data indicate an α-like mitochondrial ancestor in the willistoni subgroup, with the β mitotype likely acquired via introgression from an unidentified donor. We hypothesize that the selfish characteristics of α2 might have emerged as a response to competition for inheritance with the introgressed β mitotype.

scholarly journals New records of water mites from the Balkans revealed by DNA barcoding (Acari, Hydrachnidia)

2021 ◽  
Vol 49 ◽  
pp. 20-34
Author(s):  
Vladimir Pešić ◽  
Milica Jovanović ◽  
Ana Manović ◽  
Ioannis Karaouzas ◽  
Harry Smit
Keyword(s):  
Dna Barcoding ◽  
New Records ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
Water Mites ◽  
Water Mite ◽  
The Balkans ◽  
Coi Sequences ◽  
First Time

New records of water mites from Serbia, North Macedonia and Greece revealed by DNA barcoding are presented. DNA barcodes were recovered from 63 water mite specimens morphologically assigned to 32 species. One species Lebertia algeriensis Lundblad, 1942, is reported for the first time for the Balkans; four species, i.e. Lebertia fimbriata Thor, 1899, L. rivulorum K. Viets, 1933, Atractides stankovici Pešić & Gerecke, 2010, and Wettina lacustris Pešić & Smit, 2018 are new for North Macedonia; Monatractides madritensis (K. Viets, 1930) and Mideopsis roztoczensis Biesiadka & Kowalik, 1979 are new for Serbia; and Hygrobates mediterraneus Pešić, 2020 is new for Greece. Comparing sequences of our study with the available COI sequences we recognized five possible cases of cryptic diversity involving species clusters with more than 5% divergence indicating that these species need further study.

scholarly journals Fundamental Difficulties Prevent the Reconstruction of the Deep Phylogeny of Viruses

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1130 ◽  
Author(s):  
Jean-Michel Claverie
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Environmental Virology ◽  
Fundamental Limitations ◽  
Intracellular Parasites ◽  
Virion Structure ◽  
Agricultural Applications ◽  
History Of ◽  
High Level ◽  
Biological Entities

The extension of virology beyond its traditional medical, veterinary, or agricultural applications, now called environmental virology, has shown that viruses are both the most numerous and diverse biological entities on Earth. In particular, virus isolations from unicellular eukaryotic hosts (heterotrophic and photosynthetic protozoans) revealed numerous viral types previously unexpected in terms of virion structure, gene content, or mode of replication. Complemented by large-scale metagenomic analyses, these discoveries have rekindled interest in the enigma of the origin of viruses, for which a description encompassing all their diversity remains not available. Several laboratories have repeatedly tackled the deep reconstruction of the evolutionary history of viruses, using various methods of molecular phylogeny applied to the few shared “core” genes detected in certain virus groups (e.g., the Nucleocytoviricota). Beyond the practical difficulties of establishing reliable homology relationships from extremely divergent sequences, I present here conceptual arguments highlighting several fundamental limitations plaguing the reconstruction of the deep evolutionary history of viruses, and even more the identification of their unique or multiple origin(s). These arguments also underline the risk of establishing premature high level viral taxonomic classifications. Those limitations are direct consequences of the random mechanisms governing the reductive/retrogressive evolution of all obligate intracellular parasites.

Preserving the evolutionary history of freshwater biota in Iberian National Parks

2013 ◽  
Vol 162 ◽  
pp. 116-126 ◽  
Author(s):  
Pedro Abellán ◽  
David Sánchez-Fernández ◽  
Félix Picazo ◽  
Andrés Millán ◽  
Jorge M. Lobo ◽  
...  
Keyword(s):  
National Parks ◽  
Evolutionary History ◽  
Freshwater Biota ◽  
History Of

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.

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