scholarly journals Whole genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

2017 ◽  
Author(s):  
Milan Malinsky ◽  
Hannes Svardal ◽  
Alexandra M. Tyers ◽  
Eric A. Miska ◽  
Martin J. Genner ◽  
...  
Keyword(s):  
Gene Flow ◽  
Fish Species ◽  
Phylogenetic Analyses ◽  
Cichlid Fish ◽  
Sequence Divergence ◽  
Single Species ◽  
Lake Malawi ◽  
Genomic Diversity ◽  
Average Sequence Divergence ◽  
Deep Water Species

AbstractThe hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individuals covering 73 species across all major lineages. Average sequence divergence between species pairs is only 0.1-0.25%. These divergence values overlap diversity within species, with 82% of heterozygosity shared between species. Phylogenetic analyses suggest that diversification initially proceeded by serial branching from a generalistAstatotilapia-likeancestor. However, no single species tree adequately represents all species relationships, with evidence for substantial gene flow at multiple times. Common signatures of selection on visual and oxygen transport genes shared by distantly related deep water species point to both adaptive introgression and independent selection. These findings enhance our understanding of genomic processes underlying rapid species diversification, and provide a platform for future genetic analysis of the Malawi radiation.One Sentence Summary: The genomes of 73 cichlid fish species from Lake Malawi uncover evolutionary processes underlying a large adaptive evolutionary radiation.

scholarly journals A Population Genetics-Based and Phylogenetic Approach to Understanding the Evolution of Virulence in the Genus Listeria

2010 ◽  
Vol 76 (18) ◽  
pp. 6085-6100 ◽  
Author(s):  
Henk C. den Bakker ◽  
Brittany N. Bundrant ◽  
Esther D. Fortes ◽  
Renato H. Orsi ◽  
Martin Wiedmann
Keyword(s):  
Gene Cluster ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Virulence Gene ◽  
Selective Advantage ◽  
Opportunistic Pathogens ◽  
Evolution Of Virulence ◽  
Average Sequence Divergence ◽  
Phylogeny And Evolution ◽  
Environmental Pathogens

ABSTRACT The genus Listeria includes (i) the opportunistic pathogens L. monocytogenes and L. ivanovii, (ii) the saprotrophs L. innocua, L. marthii, and L. welshimeri, and (iii) L. seeligeri, an apparent saprotroph that nevertheless typically contains the prfA virulence gene cluster. A novel 10-loci multilocus sequence typing scheme was developed and used to characterize 67 isolates representing six Listeria spp. (excluding L. grayi) in order to (i) provide an improved understanding of the phylogeny and evolution of the genus Listeria and (ii) use Listeria as a model to study the evolution of pathogenicity in opportunistic environmental pathogens. Phylogenetic analyses identified six well-supported Listeria species that group into two main subdivisions, with each subdivision containing strains with and without the prfA virulence gene cluster. Stochastic character mapping and phylogenetic analysis of hly, a gene in the prfA cluster, suggest that the common ancestor of the genus Listeria contained the prfA virulence gene cluster and that this cluster was lost at least five times during the evolution of Listeria, yielding multiple distinct saprotrophic clades. L. welshimeri, which appears to represent the most ancient clade that arose from an ancestor with a prfA cluster deletion, shows a considerably lower average sequence divergence than other Listeria species, suggesting a population bottleneck and a putatively different ecology than other saprotrophic Listeria species. Overall, our data suggest that, for some pathogens, loss of virulence genes may represent a selective advantage, possibly by facilitating adaptation to a specific ecological niche.

Three evolutionarily significant units for conservation in the iguanid genus Brachylophus

2006 ◽  
Vol 12 (1) ◽  
pp. 64
Author(s):  
Emma L. Burns ◽  
Brian H. Costello ◽  
Bronwyn A. Houlden
Keyword(s):  
Pacific Islands ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Conservation Priorities ◽  
Separate Species ◽  
Island Populations ◽  
Evolutionarily Significant Units ◽  
Average Sequence Divergence ◽  
History Of ◽  
South Pacific Islands

We examined phylogenetic relationships within the genus Brachylophus, which comprises two endangered iguana species endemic to the South Pacific islands of Fiji and Tonga. Genetic variation among Fijian Crested Iguanas B. vitiensis and Fijian and Tongan Banded Iguanas B. fasciatus was analysed using mitochondrial DNA (mtDNA) cytochrome b (cyt b) characterized from 35 individuals from island populations. Three distinct clades of Brachylophus were identified. The most divergent clade comprised B. fasciatus from Tonga, which supports the recognition of Tongan iguanas as a separate species. Molecular clock estimates suggested that the average sequence divergence (6.4%) between Tongan and Fijian B. fasciatus clades equated to 7 - 15.8 MY of separation, confirming that extant Brachylophus species have a long history of evolution in situ in the Fijian and Tongan archipelago. Phylogenetic analyses also revealed that Fijian B. fasciatus and B. vitiensis iguana populations were not reciprocally monophyletic. One clade comprised two mtDNA haplotypes from the Fijian islands of Monu, Monuriki, Devuilau, Waya and Yadua Taba. The other clade comprised B. fasciatus haplotypes from Kadavu and Gau, which was divergent from both the aforementioned Fijian clade (dA = 3.5%), and the Tongan clade (dA = 6.4%). In addition to mtDNA data, variation was assessed at microsatellite loci, and significant differentiation between iguana populations was detected. Based on both mtDNA and microsatellite analysis, the conservation priorities for these endangered lizards must be reassessed to protect iguanas as three distinct evolutionarily significant units.

scholarly journals Linking morphological and molecular sources to disentangle the case of Xylodon australis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Javier Fernández-López ◽  
M. Teresa Telleria ◽  
Margarita Dueñas ◽  
Mara Laguna-Castro ◽  
Klaus Schliep ◽  
...  
Keyword(s):  
New Zealand ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
R Package ◽  
Molecular Data ◽  
Historical Collections ◽  
Close Relationship ◽  
Kinship Relations ◽  
History Of ◽  
Different Sources

AbstractThe use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia–New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.

Genomic diversity of chickpea-nodulating rhizobia in Ningxia (north central China) and gene flow within symbiotic Mesorhizobium muleiense populations

2020 ◽  
Vol 43 (4) ◽  
pp. 126089 ◽  
Author(s):  
Junjie Zhang ◽  
Shanshan Peng ◽  
Yimin Shang ◽  
Brigitte Brunel ◽  
Shuo Li ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genomic Diversity ◽  
Central China ◽  
North Central

Tracing the origins of hybrids through history: monstrous cultivars and Napoléon Bonaparte’s exiled paper daisies (Asteraceae; Gnaphalieae)

2021 ◽  
Author(s):  
Timothy L Collins ◽  
Jeremy J Bruhl ◽  
Alexander N Schmidt-Lebuhn ◽  
Ian R H Telford ◽  
Rose L Andrew
Keyword(s):  
Gene Flow ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Napoleon Bonaparte ◽  
Snp Data ◽  
Cast Doubt ◽  
Molecular Phylogenetic ◽  
St Helena ◽  
New Evidence

Abstract Golden everlasting paper daisies (Xerochrysum, Gnaphalieae, Asteraceae) were some of the earliest Australian native plants to be cultivated in Europe. Reputedly a favourite of Napoléon Bonaparte and Empress Joséphine, X. bracteatum is thought to have been introduced to the island of St Helena in the South Atlantic during Napoléon’s exile there. Colourful cultivars were developed in the 1850s, and there is a widely held view that these were produced by crossing Xerochrysum with African or Asian Helichrysum spp. Recent molecular phylogenetic analyses and subtribal classification of Gnaphalieae cast doubt on this idea. Using single-nucleotide polymorphism (SNP) data, we looked for evidence of gene flow between modern cultivars, naturalized paper daisies from St Helena and four Xerochrysum spp. recorded in Europe in the 1800s. There was strong support for gene flow between cultivars and X. macranthum. Paper daisies from St Helena were genotypically congruent with X. bracteatum and showed no indications of ancestry from other species or from the cultivars, consistent with the continuous occurrence of naturalized paper daisies introduced by Joséphine and Napoléon. We also present new evidence for the origin of colourful Xerochrysum cultivars and hybridization of congeners in Europe from Australian collections.

scholarly journals Checklist and practical identification key for the cichlid fishes (Cichliformes: Cichlidae) of the La Plata drainage in Bolivia, including three new geographical records

2019 ◽  
Author(s):  
Pascal I. Hablützel ◽  
Robert B. Huanto
Keyword(s):  
Fish Species ◽  
Cichlid Fish ◽  
Identification Key ◽  
Museum Collections ◽  
Additional Species ◽  
Cichlid Fishes ◽  
La Plata ◽  
Bolivian Amazon ◽  
Voucher Specimens ◽  
Historia Natural

AbstractIn comparison with the Bolivian Amazon, the ichthyofauna of the La Plata drainage of Bolivia received relatively little attention historically. Until now, 14 species of cichlid fish have been registered from this area. After an exhaustive review of museum collections (Museo de Historia Natural Noel Kempff Mercado y Colección Boliviana de Fauna), we can report three additional species: Astronotus crassipinnis (Heckel, 1840), Mesonauta festivus (Heckel, 1840) and Satanoperca pappaterra (Heckel, 1840). Four other species, which have been listed in previous publications, can be confirmed for the La Plata drainage of Bolivia based on the examination of voucher specimens: Aequidens plagiozonatus Kullander, 1984, Apistogramma commbrae (Regan, 1906), A. trifasciata (Eigenmann & Kennedy, 1903) and Crenicichla vittata Heckel, 1840. As such, 16 of the 17 species can be referenced with voucher specimens in museum collections. We also provide an identification key for the cichlid fish species of the study area.

The community structure of larval fish populations in an area of the Celtic Sea in 1998

2002 ◽  
Vol 82 (4) ◽  
pp. 641-648 ◽  
Author(s):  
S. Acevedo ◽  
O. Dwane ◽  
J.M. Fives
Keyword(s):  
Community Structure ◽  
Fish Species ◽  
Larval Fish ◽  
Single Species ◽  
Coastal Fish ◽  
Larval Stages ◽  
Celtic Sea ◽  
Sea Area ◽  
Insight Into ◽  
Fish Distributions

Ichthyoplankton from an area in the Celtic Sea was studied to provide an insight into the fish larval community structure in March, May and June 1998. Three station groups were defined each month, Neritic, Transition and Oceanic. The Neritic assemblages included larval stages of coastal fish species and the Oceanic assemblages included mesopelagic and high-oceanic fish species which were not recorded from any of the Neritic stations. The Transition stations usually contained species characteristic of both the Neritic and Oceanic assemblages. It is suggested that these broad patterns of larval fish distributions are constant features of the Celtic Sea area, probably related to the spawning location of the adults. The area is, in general, species poor, with the Oceanic stations usually dominated by a single species, indicating the presence of a large spawning school of fish.

Aestuariisphingobium litorale Li et al. 2020 is a later heterotypic synonym of Chakrabartia godavariana Jani et al. 2019

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Peng Wang ◽  
Yuxin Gao
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
Rrna Gene ◽  
Genomic Comparison ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Chakrabartia godavariana PRB40T was compared with Aestuariisphingobium litorale SYSU M10002T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of C. godavariana PRB40T had high similarity (99.8 %) to that of A. litorale SYSU M10002T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Chakrabartia . A draft genomic comparison between the two strains revealed an average nucleotide identity of 97.3 % and a digital DNA–DNA hybridization estimate of 79.5±2.9 %, strongly indicating that the two strains represented a single species. In addition, neither strain displayed any striking differences in metabolic, physiological or chemotaxonomic features. Therefore, we propose that Aestuariisphingobium litorale is a later heterotypic synonym of Chakrabartia godavariana .

scholarly journals Implementing Large Genomic Single Nucleotide Polymorphism Data Sets in Phylogenetic Network Reconstructions: A Case Study of Particularly Rapid Radiations of Cichlid Fish

2020 ◽  
Vol 69 (5) ◽  
pp. 848-862 ◽  
Author(s):  
Melisa Olave ◽  
Axel Meyer
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Gene Flow ◽  
Genetic Material ◽  
Cichlid Fish ◽  
Phylogenetic Network ◽  
Phylogenetic Networks ◽  
Nucleotide Polymorphism ◽  
Rapid Radiation ◽  
Data Set ◽  
Single Nucleotide

Abstract The Midas cichlids of the Amphilophus citrinellus spp. species complex from Nicaragua (13 species) are an extraordinary example of adaptive and rapid radiation ($<$24,000 years old). These cichlids are a very challenging group to infer its evolutionary history in phylogenetic analyses, due to the apparent prevalence of incomplete lineage sorting (ILS), as well as past and current gene flow. Assuming solely a vertical transfer of genetic material from an ancestral lineage to new lineages is not appropriate in many cases of genes transferred horizontally in nature. Recently developed methods to infer phylogenetic networks under such circumstances might be able to circumvent these problems. These models accommodate not just ILS, but also gene flow, under the multispecies network coalescent (MSNC) model, processes that are at work in young, hybridizing, and/or rapidly diversifying lineages. There are currently only a few programs available that implement MSNC for estimating phylogenetic networks. Here, we present a novel way to incorporate single nucleotide polymorphism (SNP) data into the currently available PhyloNetworks program. Based on simulations, we demonstrate that SNPs can provide enough power to recover the true phylogenetic network. We also show that it can accurately infer the true network more often than other similar SNP-based programs (PhyloNet and HyDe). Moreover, our approach results in a faster algorithm compared to the original pipeline in PhyloNetworks, without losing power. We also applied our new approach to infer the phylogenetic network of Midas cichlid radiation. We implemented the most comprehensive genomic data set to date (RADseq data set of 679 individuals and $>$37K SNPs from 19 ingroup lineages) and present estimated phylogenetic networks for this extremely young and fast-evolving radiation of cichlid fish. We demonstrate that the MSNC is more appropriate than the multispecies coalescent alone for the analysis of this rapid radiation. [Genomics; multispecies network coalescent; phylogenetic networks; phylogenomics; RADseq; SNPs.]

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