Insights into the Migration Routes and Historical Dispersion of Species Surviving the Messinian Crisis: The Case of Patella ulyssiponensis and Epizoic Rhodolith Lithophyllum hibernicum

The genus Patella (Patellogastropoda, Mollusca) is represented by a group of species exclusive to the Northeast Atlantic Ocean (including Macaronesian archipelagos) and Mediterranean Sea. The species Patella ulyssiponensis and Patella aspera are common in European waters, with the first inhabiting continental coast, and the second endemic to Macaronesian archipelagos. However, the acceptance of these two lineages as separate species is still highly debated. The red coralline species algae Lithophyllum hibernicum, distributed from Northeast Atlantic to the Mediterranean, is usually found as epilithic crusts or unattached forms (named rhodolith beds), although it also forms epizoic crusts on other organisms, e.g., shell surfaces. In order to study the historic dispersal and migration routes of the Patella ulyssiponensis-aspera complex, taxonomic, genetic and biogeographic approaches were employed based on haplotype network analyses and estimations for the most common recent ancestor (TMRCA), using Cytochrome Oxydase I. A synonymy for these two species is proposed, with the presence of a shared haplotype between the continental (P. ulyssiponensis) and insular (P. aspera) lineages, and with basis of morphological and nomenclatural data. We propose an evolutionary scenario for its dispersal based on a high haplotype diversity for the Mediterranean regions, indicating its possible survival during the Messinian Salinity Crisis (6–5.3 Mya), followed by a colonization of the Proto-Macaronesian archipelagos. The epizoic association of L. hibernicum on P. ulyssiponensis shell adult surface is recorded in this study, likewise the promotion of settlement conditions provided by these coralline algae to P. ulyssiponensis larvae, may explain the reach of P. ulyssiponensis distribution through rhodolith transportation.

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Convergent evolution in Cladonia gracilis and allies

The Lichenologist ◽

10.1017/s0024282909990569 ◽

2010 ◽

Vol 42 (3) ◽

pp. 323-338 ◽

Cited By ~ 19

Author(s):

Kyle M. FONTAINE ◽

Teuvo AHTI ◽

Michele D. PIERCEY-NORMORE

Keyword(s):

Convergent Evolution ◽

Species Complex ◽

Polyketide Synthase ◽

Its Region ◽

Haplotype Network ◽

Amino Acid Sequences ◽

Nuclear Ribosomal Dna ◽

Morphological Similarity ◽

Separate Species ◽

Network Analyses

AbstractMembers of the Cladonia gracilis group of lichen fungi are common terrestrial lichens where morphological features are more similar between members of the C. gracilis species complex and allied species outside the complex than they are between subspecies within the complex. The objectives of this study were to examine whether the Cladonia gracilis species complex is monophyletic, to determine whether morphological similarity is supported by genetic variation, and to examine the utility of the polyketide synthase (PKS) gene for phylogenetic studies among closely related species. Two loci, the ketosynthase region of the PKS gene and the internal transcribed spacer (ITS) region of nuclear ribosomal DNA, were sequenced and analysed by Maximum Parsimony, Bayesian and haplotype network analyses. Functional differences were also inferred through ITS2 RNA secondary structures and non-synonymous changes in translated PKS amino acid sequences. The monophyly of the C. gracilis complex is supported by 71% bootstrap in the ITS phylogeny, and 92% bootstrap with greater than 95% posterior probability in the PKS phylogeny. Morphological similarity is not always supported by genetic similarity. The PKS gene is less variable than the ITS but the PKS supports species hypotheses that are reflected in the ITS2 RNA model. We conclude that monophyly of the C. gracilis complex can be supported if C. cornuta, C. coniocraea and C. ochrochlora are included in the complex. In addition, C. maxima, C. phyllophora and C. subchordalis are supported as monophyletic species outside the C. gracilis complex. Cladonia maxima may form a separate species and variation among podetial morphology may be explained by convergent evolution.

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Genetic diversity and variation of seven Chinese grass shrimp (Palaemonetes sinensis) populations based on the mitochondrial COI gene

BMC Ecology and Evolution ◽

10.1186/s12862-021-01893-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yingying Zhao ◽

Xiaochen Zhu ◽

Ye Jiang ◽

Zhi Li ◽

Xin Li ◽

...

Keyword(s):

Genetic Diversity ◽

Demographic History ◽

Haplotype Diversity ◽

Grass Shrimp ◽

Haplotype Network ◽

Coi Gene ◽

Wild Populations ◽

Important Species ◽

Network Analyses ◽

Maximum Variation

Abstract Background Chinese grass shrimp (Palaemonetes sinensis) is an important species widely distributed throughout China, which is ecologically relevant and possesses ornamental and economic value. These organisms have experienced a sharp decline in population due to overfishing. Therefore interest in P. sinensis aquaculture has risen in an effort to alleviate fishing pressure on wild populations. Therefore, we investigated the genetic diversity and variation of P. sinensis to verify the accuracy of previous research results, as well as to assess the risk of diversity decline in wild populations and provide data for artificial breeding. Methods Palaemonetes sinensis specimens from seven locations were collected and their genetic variability was assessed based on mitochondrial COI gene segments. DNA sequence polymorphisms for each population were estimated using DNASP 6.12. The demographic history and genetic variation were evaluated using Arlequin 3.11. At last, the pairwise genetic distance (Ds) values and dendrograms were constructed with the MEGA 11 software package. Results Our study obtained sequences from 325 individuals, and 41 haplotypes were identified among the populations. The haplotype diversity (Hd) and nucleotide diversity (π) indices ranged from 0.244 ± 0.083 to 0.790 ± 0.048 and from 0.0004 ± 0.0001 to 0.0028 ± 0.0006, respectively. Haplotype network analyses identified haplotype Hap_1 as a potential maternal ancestral haplotype for the studied populations. AMOVA results indicated that genetic variations mainly occurred within populations (73.07%). Moreover, according to the maximum variation among groups (FCT), analysis of molecular variance using the optimal two-group scheme indicated that the maximum variation occurred among groups (53.36%). Neutrality and mismatch distribution tests suggested that P. sinensis underwent a recent population expansion. Consistent with the SAMOVA analysis and haplotype network analyses, the Ds and FST between the population pairs indicated that the JN population was distinctive from the others. Conclusions Our study conducted a comprehensive characterization of seven wild P. sinensis populations, and our findings elucidated highly significant differences within populations. The JN population was differentiated from the other six populations, as a result of long-term geographical separation. Overall, the present study provided a valuable basis for the management of genetic resources and a better understanding of the ecology and evolution of this species.

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Genetic diversity and its conservation implications of Vitex rotundifolia (Lamiaceae) populations in East Asia

PeerJ ◽

10.7717/peerj.6194 ◽

2019 ◽

Vol 7 ◽

pp. e6194 ◽

Cited By ~ 4

Author(s):

Yiqi Sun ◽

Hong Yang ◽

Qiaoyan Zhang ◽

Luping Qin ◽

Pan Li ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Population Differentiation ◽

Haplotype Diversity ◽

Haplotype Network ◽

Conservation Strategy ◽

Nuclear Ribosomal Dna ◽

Wild Plants ◽

Intergenic Spacers ◽

Network Analyses

Vitex rotundifolia is an important coastal and medicinal plant, and is recorded in the List of the Important Wild Plants for Conservation in China and Japan. However, an effective conservation strategy is lacking. In the present study, the genetic diversity and population structure were analyzed using phylogeographical methods based on the trnH-psbA and trnG-trnS intergenic spacers of the chloroplast DNA (cpDNA) sequences from 157 individuals from 25 sampling sites for V. rotundifolia and V. trifolia plus the internal transcribed spacer (ITS) of the nuclear ribosomal DNA (nrDNA) sequences of 177 individuals from 27 sampling sites. The results showed that V. rotundifolia and V. trifolia had eight cpDNA and two nrDNA haplotypes, respectively, and the V. rotundifolia has a low level of genetic diversity (haplotype diversity hd,cp = 0.360, hd,nr = 0.440), a more pronounced genetic differentiation among populations (population differentiation at the species level (GST) = 0.201, population differentiation at the allele level (NST) = 0.462), and an insignificantly different phylogeographical structure (NST > GST, P > 0.05). In addition, haplotype network analyses indicated that V. rotundifolia and V. trifolia have distinct haplotypes. Divergence dating based on BEAST software analyses showed that most cpDNA clades diverged in the late Pleistocene era. Demographic analysis indicated that V. rotundifolia underwent a rapid demographic expansion. Some scientific strategies are suggested for resource conservation of V. rotundifolia based on its genetic diversity and population structure.

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Cryptic speciation in the Warbling Vireo (Vireo gilvus)

The Auk ◽

10.1093/ornithology/ukaa071 ◽

2021 ◽

Author(s):

Scott F Lovell ◽

M Ross Lein ◽

Sean M Rogers

Keyword(s):

Contact Zone ◽

Nuclear Dna ◽

Biological Species ◽

Valid Species ◽

Migration Routes ◽

Dna Evidence ◽

Show Evidence ◽

And Migration ◽

Surrounding Areas ◽

Taxonomic Groups

Abstract Eastern (Vireo gilvus gilvus) and western (V. g. swainsoni) forms of the Warbling Vireo have essentially allopatric breeding ranges across north-central North America, but come into contact in central Alberta, Canada. In 1986, Jon Barlow presented preliminary morphological and song evidence suggesting that the Warbling Vireo complex might comprise more than one valid species. However, to date, Barlow’s suggestion is supported by only limited DNA evidence, demonstration of molt and migration differences between the taxa, and anecdotal accounts of differences in song, morphology, plumage, and ecology. We analyzed variation in both mitochondrial and nuclear DNA in birds from Alberta and surrounding areas to determine the levels of genetic differentiation and hybridization occurring in the contact zone, and whether the two taxa warrant recognition as separate biological species. Our analyses reveal that Warbling Vireos in Alberta and the surrounding areas are separated into two well-defined, genetically differentiated, and monophyletic clades corresponding to previously recognized taxonomic groups. The two taxa come into contact in a narrow (~85 km) zone in Barrhead County, northwest of Edmonton, Alberta. They show evidence of limited hybridization. The distinct genetic differences are maintained in the contact zone, where individuals of the two taxa may occupy neighboring territories. Differences in spring arrival dates, molt schedules, and migration routes indicate that a migratory divide may play an important role in reproductive isolation. We suggest that the two taxa are distinct cryptic species: an eastern form, Vireo gilvus, and a western form, Vireo swainsoni.

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Genetic variability and demographic history of Heliothis virescens (Lepidoptera: Noctuidae) populations from Brazil inferred by mtDNA sequences

Bulletin of Entomological Research ◽

10.1017/s0007485311000678 ◽

2011 ◽

Vol 102 (3) ◽

pp. 333-343 ◽

Cited By ~ 16

Author(s):

K.C. Albernaz ◽

K.L. Silva-Brandão ◽

P. Fresia ◽

F.L. Cônsoli ◽

C. Omoto

Keyword(s):

Genetic Structure ◽

Genetic Variability ◽

Heliothis Virescens ◽

Demographic History ◽

Haplotype Diversity ◽

Low Frequency ◽

Haplotype Network ◽

Demographic Expansion ◽

Significant Genetic Structure ◽

History Of

AbstractIntra- and inter-population genetic variability and the demographic history of Heliothis virescens (F.) populations were evaluated by using mtDNA markers (coxI, coxII and nad6) with samples from the major cotton- and soybean-producing regions in Brazil in the growing seasons 2007/08, 2008/09 and 2009/10. AMOVA indicated low and non-significant genetic structure, regardless of geographical scale, growing season or crop, with most of genetic variation occurring within populations. Clustering analyzes also indicated low genetic differentiation. The haplotype network obtained with combined datasets resulted in 35 haplotypes, with 28 exclusive occurrences, four of them sampled only from soybean fields. The minimum spanning network showed star-shaped structures typical of populations that underwent a recent demographic expansion. The recent expansion was supported by other demographic analyzes, such as the Bayesian skyline plot, the unimodal distribution of paired differences among mitochondrial sequences, and negative and significant values of neutrality tests for the Tajima's D and Fu's FS parameters. In addition, high values of haplotype diversity (Ĥ) and low values of nucleotide diversity (π), combined with a high number of low frequency haplotypes and values of θπ<θW, suggested a recent demographic expansion of H. virescens populations in Brazil. This demographic event could be responsible for the low genetic structure currently found; however, haplotypes present uniquely at the same geographic regions and from one specific host plant suggest an initial differentiation among H. virescens populations within Brazil.

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Revised distribution and phytosociological data of Orobanche coerulescens Stephan in Willd. (Orobanchaceae): Poland in relation to Central Europe

Biodiversity Research and Conservation ◽

10.2478/v10119-012-0007-4 ◽

2012 ◽

Vol 26 (1) ◽

pp. 61-72 ◽

Cited By ~ 4

Author(s):

Renata Piwowarczyk

Keyword(s):

Eastern Europe ◽

Central Europe ◽

Plant Communities ◽

Field Research ◽

Range Limits ◽

Migration Routes ◽

Original Field ◽

Critical Revision ◽

And Migration ◽

North Western

Abstract Orobanche coerulescens has a Eurasian distribution. The species is classified as extinct at most of its localities at the western limit of its range. Its populations are very scarce and critically endangered in Central Europe. This work presents the current distribution of O.coerulescens in Poland, based on a critical revision of herbarium and literature data as well as results of original field research, and reviews its distribution in Central Europe (partly in Eastern Europe). Habitats, plant communities, and migration routes of O.coerulescens in Central Europe are discussed. The species was initially known in Poland from now historical localities in Pomerania and the valley of the lower Vistula. In 2000-2011 it was recorded at 9 localities in Podlasie, the Małopolska Upland (Wyżyna Małopolska), and the Łódź Hills (Wzniesienia Łódzkie). Its abundance at the localities ranged from a few to over 1000 shoots. These are the largest populations of O.coerulescens at its western and north-western range limits.

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Phylogenetic and Haplotype Network Analyses of Diaporthe eres Species in China Based on Sequences of Multiple Loci

Biology ◽

10.3390/biology10030179 ◽

2021 ◽

Vol 10 (3) ◽

pp. 179

Author(s):

Chingchai Chaisiri ◽

Xiangyu Liu ◽

Yang Lin ◽

Yanping Fu ◽

Fuxing Zhu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Elongation Factor ◽

Haplotype Network ◽

Population Diversity ◽

Plant Diseases ◽

Broad Host Range ◽

Internal Transcribed Spacer Region ◽

Chinese Populations ◽

Network Analyses ◽

Haplotype Networks

Diaporthe eres is considered one of the most important causal agents of many plant diseases, with a broad host range worldwide. In this study, multiple sequences of ribosomal internal transcribed spacer region (ITS), translation elongation factor 1-α gene (EF1-α), beta-tubulin gene (TUB2), calmodulin gene (CAL), and histone-3 gene (HIS) were used for multi-locus phylogenetic analysis. For phylogenetic analysis, maximum likelihood (ML), maximum parsimony (MP), and Bayesian inferred (BI) approaches were performed to investigate relationships of D. eres with closely related species. The results strongly support that the D. eres species falls into a monophyletic lineage, with the characteristics of a species complex. Phylogenetic informativeness (PI) analysis showed that clear boundaries could be proposed by using EF1-α, whereas ITS showed an ineffective reconstruction and, thus, was unsuitable for speciating boundaries for Diaporthe species. A combined dataset of EF1-α, CAL, TUB2, and HIS showed strong resolution for Diaporthe species, providing insights for the D. eres complex. Accordingly, besides D. biguttusis, D. camptothecicola, D. castaneae-mollissimae, D. cotoneastri, D. ellipicola, D. longicicola, D. mahothocarpus, D. momicola, D. nobilis, and Phomopsis fukushii, which have already been previously considered the synonymous species of D. eres, another three species, D. henanensis, D. lonicerae and D. rosicola, were further revealed to be synonyms of D. eres in this study. In order to demonstrate the genetic diversity of D. eres species in China, 138 D. eres isolates were randomly selected from previous studies in 16 provinces. These isolates were obtained from different major plant species from 2006 to 2020. The genetic distance was estimated with phylogenetic analysis and haplotype networks, and it was revealed that two major haplotypes existed in the Chinese populations of D. eres. The haplotype networks were widely dispersed and not uniquely correlated to specific populations. Overall, our analyses evaluated the phylogenetic identification for D. eres species and demonstrated the population diversity of D. eres in China.

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Automated monitoring of a large-scale cod (Gadus morhua) migration in the open sea

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f02-152 ◽

2002 ◽

Vol 59 (12) ◽

pp. 1845-1850 ◽

Cited By ~ 35

Author(s):

Luc A Comeau ◽

Steven E Campana ◽

Martin Castonguay

Keyword(s):

Large Scale ◽

Gadus Morhua ◽

Atlantic Cod ◽

Seasonal Migration ◽

Migration Routes ◽

Eastern Canada ◽

Migration Patterns ◽

Migration Timing ◽

Open Sea ◽

And Migration

The migration patterns of marine fishes are poorly known, in part owing to the technical limitations associated with tracking the movements of animals in deep water. Here we document a large-scale, directed, migration of Atlantic cod (Gadus morhua) off eastern Canada. Our approach was based on the acoustic tagging of 126 fish and the deployment of 69 subsurface receivers, stretching over a 160-km distance along the edge of the Laurentian Channel. After 1 year of automated recording, we found that 65% of the fish migrated out of coastal waters in two distinct runs during the summerautumn period. The offshore-migrating fish overwintered in deep Laurentian Channel waters, returning inshore in April. Individual migration routes and migration timing were variable, indicating that the cod did not aggregate in large schools during the seasonal migration events.

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Genetic flow among olive populations within the Mediterranean basin

PeerJ ◽

10.7717/peerj.5260 ◽

2018 ◽

Vol 6 ◽

pp. e5260 ◽

Cited By ~ 14

Author(s):

Valentina di Rienzo ◽

Sara Sion ◽

Francesca Taranto ◽

Nunzio D’Agostino ◽

Cinzia Montemurro ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Resources ◽

Mediterranean Basin ◽

Eastern Mediterranean ◽

Olive Tree ◽

Gene Pools ◽

The North ◽

The Mediterranean ◽

And Migration ◽

The Mediterranean Basin

Background The olive tree is a typical crop of the Mediterranean basin where it shows a wide diversity, accounting for more than 2,600 cultivars. The ability to discriminate olive cultivars and determine their genetic variability is pivotal for an optimal exploitation of olive genetic resources. Methods We investigated the genetic diversity within 128 olive accessions belonging to four countries in the Mediterranean Basin (Italy, Algeria, Syria, and Malta), with the purpose of better understanding the origin and spread of the olive genotypes across Mediterranean Basin countries. Eleven highly polymorphic simple sequence repeat (SSR) markers were used and proved to be very informative, producing a total of 179 alleles. Results Cluster analysis distinguished three main groups according to their geographical origin, with the current sample of Maltese accessions included in the Italian group. Phylogenetic analysis further differentiated Italian and Maltese olive accessions, clarifying the intermediate position of Maltese accessions along the x/y-axes of principal coordinate analysis (PCoA). Model-based and neighbor clustering, PCoA, and migration analysis suggested the existence of two different gene pools (Algerian and Syrian) and that the genetic exchange occurred between the Syrian, Italian and Maltese populations. Discussion The close relationship between Syrian and Italian and Maltese olives was consistent with the historical domestication and migration of olive tree from the North Levant to eastern Mediterranean basin. This study lays the foundations for a better understanding of olive genetic diversity in the Mediterranean basin and represents a step toward an optimal conservation and exploitation of olive genetic resources.

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Overlapping effects of miR-21 inhibition and drugs for idiopathic pulmonary fibrosis in the post-myocardial infarction setting

European Heart Journal ◽

10.1093/eurheartj/ehab724.1313 ◽

2021 ◽

Vol 42 (Supplement_1) ◽

Author(s):

A Aimo ◽

O Iborra Egea ◽

C Passino ◽

M Emdin

Keyword(s):

Idiopathic Pulmonary Fibrosis ◽

Pulmonary Fibrosis ◽

Protein Interactions ◽

Target Genes ◽

Cardiac Fibrosis ◽

Biological Significance ◽

Oral Drugs ◽

Network Analyses ◽

Funding Sources ◽

And Migration

Abstract Background Intracoronary infusion of a specific miR-21 inhibitor after reperfused MI has been reported to reduce cardiac fibrosis and hypertrophy and improve cardiac function in pigs. Possible drawbacks of anti-miR-21 therapy are the high costs of this therapy, and the need for intracoronary administration, preferably some days after reperfusion. Oral drugs with anti-fibrotic actions could have similar effects than anti-miR-21, while overcoming the limitations of anti-miR-21. We tested this hypothesis by examining the two oral drugs approved for idiopathic pulmonary fibrosis (nintedanib and pirfenidone). Methods We identified the regulatory profile of miR-21, which included 588 target genes. Only 99 of these interactions were supported by information from reporter gene assays. The biological significance of these 99 targets was evaluated through over-representation analysis, and 13 genes were identified as potentially related to cardiovascular diseases. We retrieved all known targets and main downstream interactions of nintedanib and pirfenidone from Drugbank. Finally, we cross-validated these datasets by using neural network analyses to search for protein-protein interactions, focusing on those shared by miR-21 inhibition, nintedanib and pirfenidone. Results Nintedanib and anti-miR21 had many targets in common, which could indicate an overlap in their corresponding mechanisms of action. The proto-oncogene SRC, which participates in gene transcription, immune response, apoptosis and migration, emerged as the leading signaling effector. By blocking SRC expression and many downstream effectors of SRC, as well as platelet-derived growth factor, nintedanib could decreased miR-21 expression. The molecular effects of nintedanib include inhibition of inflammation, fibrosis and angiogenesis, and then ultimately a relief from I/R injury, in a similar fashion than anti-miR-21. Contrary to nintedanib, no overlap between the effects of pirfenidone and anti-miR-21 was found. Conclusion Because of the remarkably strong overlapping with the targets of miR-21, there is a stronger rationale to assess nintedanib than pirfenidone as a cardioprotective therapy. If confirmed by experimental evidence, nintedanib could enter the stage of clinical trials to assess its efficacy in human patients with STEMI. Funding Acknowledgement Type of funding sources: None.

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