New insights into the genetic diversity of the stone crayfish: taxonomic and conservation implications

Abstract Background Austropotamobius torrentium is a freshwater crayfish species native to central and south-eastern Europe, with an intricate evolutionary history and the highest genetic diversity recorded in the northern-central Dinarides (NCD). Its populations are facing declines, both in number and size across its entire range. By extanding current knowledge on the genetic diversity of this species, we aim to assist conservation programmes. Multigene phylogenetic analyses were performed using different divergence time estimates based on mitochondrial and, for the first time, nuclear DNA markers on the largest data set analysed so far. In order to reassess taxonomic relationships within this species we applied several species delimitation methods and studied the meristic characters with the intention of finding features that would clearly separate stone crayfish belonging to different phylogroups. Results Our results confirmed the existence of high genetic diversity within A. torrentium, maintained in divergent phylogroups which have their own evolutionary dynamics. A new phylogroup in the Kordun region belonging to NCD has also been discovered. Due to the incongruence between implemented species delimitation approaches and the lack of any morphological characters conserved within lineages, we are of the opinion that phylogroups recovered on mitochondrial and nuclear DNA are cryptic subspecies and distinct evolutionary significant units. Conclusions Geographically and genetically isolated phylogroups represent the evolutionary legacy of A. torrentium and are highly relevant for conservation due to their evolutionary distinctiveness and restricted distribution.

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Molecular Evolutionary Dynamics of Respiratory Syncytial Virus Group A in Recurrent Epidemics in Coastal Kenya

Journal of Virology ◽

10.1128/jvi.03105-15 ◽

2016 ◽

Vol 90 (10) ◽

pp. 4990-5002 ◽

Cited By ~ 19

Author(s):

James R. Otieno ◽

Charles N. Agoti ◽

Caroline W. Gitahi ◽

Ann Bett ◽

Mwanajuma Ngama ◽

...

Keyword(s):

Genetic Diversity ◽

Respiratory Syncytial Virus ◽

Time Scales ◽

Evolutionary Dynamics ◽

Nucleotide Substitutions ◽

High Genetic Diversity ◽

Data Set ◽

New Variant ◽

Syncytial Virus ◽

Highest Posterior Density

ABSTRACTThe characteristic recurrent epidemics of human respiratory syncytial virus (RSV) within communities may result from the genetic variability of the virus and associated evolutionary adaptation, reducing the efficiency of preexisting immune responses. We analyzed the molecular evolutionary changes in the attachment (G) glycoprotein of RSV-A viruses collected over 13 epidemic seasons (2000 to 2012) in Kilifi (n= 649), Kenya, and contemporaneous sequences (n= 1,131) collected elsewhere within Kenya and 28 other countries. Genetic diversity in the G gene in Kilifi was dynamic both within and between epidemics, characterized by frequent new variant introductions and limited variant persistence between consecutive epidemics. Four RSV-A genotypes were detected in Kilifi: ON1 (11.9%), GA2 (75.5%), GA5 (12.3%), and GA3 (0.3%), with predominant genotype replacement of GA5 by GA2 and then GA2 by ON1. Within these genotypes, there was considerable variation in potentialN-glycosylation sites, with GA2 and ON1 viruses showing up to 15 different patterns involving eight possible sites. Further, we identified 15 positively selected and 34 genotype-distinguishing codon sites, with six of these sites exhibiting both characteristics. The mean substitution rate of the G ectodomain for the Kilifi data set was estimated at 3.58 × 10−3(95% highest posterior density interval = 3.04 to 4.16) nucleotide substitutions/site/year. Kilifi viruses were interspersed in the global phylogenetic tree, clustering mostly with Kenyan and European sequences. Our findings highlight ongoing genetic evolution and high diversity of circulating RSV-A strains, locally and globally, with potential antigenic differences. Taken together, these provide a possible explanation on the nature of recurrent local RSV epidemics.IMPORTANCEThe mechanisms underlying recurrent epidemics of RSV are poorly understood. We observe high genetic diversity in circulating strains within and between epidemics in both local and global settings. On longer time scales (∼7 years) there is sequential replacement of genotypes, whereas on shorter time scales (one epidemic to the next or within epidemics) there is a high turnover of variants within genotypes. Further, this genetic diversity is predicted to be associated with variation in antigenic profiles. These observations provide an explanation for recurrent RSV epidemics and have potential implications on the long-term effectiveness of vaccines.

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Integrated analysis of the ringneck snake Diadophis punctatus complex (Colubridae: Dipsadidae) in a biodiversity hotspot provides the foundation for conservation reassessment

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blab028 ◽

2021 ◽

Vol 133 (1) ◽

pp. 105-119

Author(s):

Frank M Fontanella ◽

Emily Miles ◽

Polly Strott

Keyword(s):

Genetic Diversity ◽

Species Delimitation ◽

Conservation Status ◽

Morphological Data ◽

Integrated Analysis ◽

Conservation Priorities ◽

Species Classification ◽

Divergence Time Estimates ◽

Diadophis Punctatus ◽

Cryptic Genetic Diversity

Abstract Species classification may not reflect the underlying/cryptic genetic diversity and focusing on groups that do not represent historically independent units can misdirect conservation efforts. The identification of evolutionarily significant units (ESUs) allows cryptic genetic diversity to be accounted for when designating conservation priorities. We used multi-locus coalescent-based species delimitation methods and multivariate analyses of morphological data to examine whether the subspecies merit conservation recognition and infer the ESUs in ringneck snakes (Diadophis punctatus) throughout the California Floristic Province. Species delimitation methods failed to recover groups consistent with designated subspecies and instead inferred three well supported, mostly geographically isolated lineages. Divergence time estimates suggest that the divergences were driven by historical isolation associated with Pleistocene climate shifts. We found a correlation between increased morphological differentiation and time since divergence, and greater niche similarity between the more recently diverged eastern California and western California groups. Based on these results, we propose that the morphological similarities are due to a combination of morphological conservatism and evolutionary stasis. Our study provides the foundation necessary to re-assess the biodiversity and conservation status of ringneck snakes and offers an important step in unveiling the diversity within the western portion of the genus’ range.

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Evolutionary Genetics of Mycobacterium tuberculosis and HIV-1: “The Tortoise and the Hare”

Microorganisms ◽

10.3390/microorganisms9010147 ◽

2021 ◽

Vol 9 (1) ◽

pp. 147

Author(s):

Ana Santos-Pereira ◽

Carlos Magalhães ◽

Pedro M. M. Araújo ◽

Nuno S. Osório

Keyword(s):

Genetic Diversity ◽

Drug Resistance ◽

Mycobacterium Tuberculosis ◽

Evolutionary Dynamics ◽

Evolutionary Genetics ◽

Host Cells ◽

Whole Genome Sequencing Data ◽

Host Immune System ◽

Viral Mutant ◽

Hiv 1

The already enormous burden caused by Mycobacterium tuberculosis and Human Immunodeficiency Virus type 1 (HIV-1) alone is aggravated by co-infection. Despite obvious differences in the rate of evolution comparing these two human pathogens, genetic diversity plays an important role in the success of both. The extreme evolutionary dynamics of HIV-1 is in the basis of a robust capacity to evade immune responses, to generate drug-resistance and to diversify the population-level reservoir of M group viral subtypes. Compared to HIV-1 and other retroviruses, M. tuberculosis generates minute levels of genetic diversity within the host. However, emerging whole-genome sequencing data show that the M. tuberculosis complex contains at least nine human-adapted phylogenetic lineages. This level of genetic diversity results in differences in M. tuberculosis interactions with the host immune system, virulence and drug resistance propensity. In co-infected individuals, HIV-1 and M. tuberculosis are likely to co-colonize host cells. However, the evolutionary impact of the interaction between the host, the slowly evolving M. tuberculosis bacteria and the HIV-1 viral “mutant cloud” is poorly understood. These evolutionary dynamics, at the cellular niche of monocytes/macrophages, are also discussed and proposed as a relevant future research topic in the context of single-cell sequencing.

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Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations

Nature Communications ◽

10.1038/s41467-021-20958-2 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

H. De Kort ◽

J. G. Prunier ◽

S. Ducatez ◽

O. Honnay ◽

M. Baguette ◽

...

Keyword(s):

Genetic Diversity ◽

Life History ◽

Evolutionary Dynamics ◽

Environmental Changes ◽

Peripheral Populations ◽

Plant Dispersal ◽

Weak Support ◽

Animal Populations ◽

Plant Groups ◽

Conservation Genetic

AbstractUnderstanding how biological and environmental factors interactively shape the global distribution of plant and animal genetic diversity is fundamental to biodiversity conservation. Genetic diversity measured in local populations (GDP) is correspondingly assumed representative for population fitness and eco-evolutionary dynamics. For 8356 populations across the globe, we report that plants systematically display much lower GDP than animals, and that life history traits shape GDP patterns both directly (animal longevity and size), and indirectly by mediating core-periphery patterns (animal fecundity and plant dispersal). Particularly in some plant groups, peripheral populations can sustain similar GDP as core populations, emphasizing their potential conservation value. We further find surprisingly weak support for general latitudinal GDP trends. Finally, contemporary rather than past climate contributes to the spatial distribution of GDP, suggesting that contemporary environmental changes affect global patterns of GDP. Our findings generate new perspectives for the conservation of genetic resources at worldwide and taxonomic-wide scales.

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Spatial pattern and genetic diversity estimates are linked in stochastic models of population differentiation

Genetics and Molecular Biology ◽

10.1590/s1415-47572000000300007 ◽

2000 ◽

Vol 23 (3) ◽

pp. 541-544 ◽

Cited By ~ 8

Author(s):

José Alexandre Felizola Diniz-Filho ◽

Mariana Pires de Campos Telles

Keyword(s):

Genetic Diversity ◽

Spatial Pattern ◽

Stochastic Models ◽

Population Differentiation ◽

Real Data ◽

Population Heterogeneity ◽

Data Set ◽

Mantel’S Test ◽

The Relationship ◽

Diversity Estimates

In the present study, we used both simulations and real data set analyses to show that, under stochastic processes of population differentiation, the concepts of spatial heterogeneity and spatial pattern overlap. In these processes, the proportion of variation among and within a population (measured by G ST and 1 - G ST, respectively) is correlated with the slope and intercept of a Mantel's test relating genetic and geographic distances. Beyond the conceptual interest, the inspection of the relationship between population heterogeneity and spatial pattern can be used to test departures from stochasticity in the study of population differentiation.

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Early and Middle Triassic trends in diversity, evenness, and size of foraminifers on a carbonate platform in south China: implications for tempo and mode of biotic recovery from the end-Permian mass extinction

Paleobiology ◽

10.1666/08082.1 ◽

2011 ◽

Vol 37 (3) ◽

pp. 409-425 ◽

Cited By ~ 57

Author(s):

Jonathan L. Payne ◽

Mindi Summers ◽

Brianna L. Rego ◽

Demir Altiner ◽

Jiayong Wei ◽

...

Keyword(s):

South China ◽

Mass Extinction ◽

Evolutionary Dynamics ◽

Middle Triassic ◽

Carbonate Platform ◽

Early Triassic ◽

Data Set ◽

Recovery Pattern ◽

Biotic Recovery ◽

Permian Mass Extinction

Delayed biotic recovery from the end-Permian mass extinction has long been interpreted to result from environmental inhibition. Recently, evidence of more rapid recovery has begun to emerge, suggesting the role of environmental inhibition was previously overestimated. However, there have been few high-resolution taxonomic and ecological studies spanning the full Early and Middle Triassic recovery interval, leaving the precise pattern of recovery and underlying mechanisms poorly constrained. In this study, we document Early and Middle Triassic trends in taxonomic diversity, assemblage evenness, and size distribution of benthic foraminifers on an exceptionally exposed carbonate platform in south China. We observe gradual increases in all metrics through Early Triassic and earliest Middle Triassic time, with stable values reached early in the Anisian. There is little support in our data set for a substantial Early Triassic lag interval during the recovery of foraminifers or for a stepwise recovery pattern. The recovery pattern of foraminifers on the GBG corresponds well with available global data for this taxon and appears to parallel that of many benthic invertebrate clades. Early Triassic diversity increase in foraminifers was more gradual than in ammonoids and conodonts. However, foraminifers continued to increase in diversity, size, and evenness into Middle Triassic time, whereas diversity of ammonoids and conodonts declined. These contrasts suggest decoupling of recovery between benthic and pelagic environments; it is unclear whether these discrepancies reflect inherent contrasts in their evolutionary dynamics or the differential impact of Early Triassic ocean anoxia or associated environmental parameters on benthic ecosystems.

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Minimal clustering and species delimitation based on multi-locus alignments vs SNPs: the case of the Seriphium plumosum L. complex (Gnaphalieae: Asteraceae)

10.1101/2021.03.21.436318 ◽

2021 ◽

Author(s):

Zaynab Shaik ◽

Nicola Georgina Bergh ◽

Bengt Oxelman ◽

Anthony George Verboom

Keyword(s):

Species Delimitation ◽

Bayes Factor ◽

Cape Floristic Region ◽

Parametric Models ◽

Western Cape ◽

Nucleotide Polymorphisms ◽

Sequence Alignments ◽

Separate Species ◽

Multiple Sequence ◽

Data Set

We applied species delimitation methods based on the Multi-Species Coalescent (MSC) model to 500+ loci derived from genotyping-by-sequencing on the South African Seriphium plumosum (Asteraceae) species complex. The loci were represented either as multiple sequence alignments or single nucleotide polymorphisms (SNPs), and analysed by the STACEY and Bayes Factor Delimitation (BFD)/SNAPP methods, respectively. Both methods supported species taxonomies where virtually all of the 32 sampled individuals, each representing its own geographical population, were identified as separate species. Computational efforts required to achieve adequate mixing of MCMC chains were considerable, and the species/minimal cluster trees identified similar strongly supported clades in replicate runs. The resolution was, however, higher in the STACEY trees than in the SNAPP trees, which is consistent with the higher information content of full sequences. The computational efficiency, measured as effective sample sizes of likelihood and posterior estimates per time unit, was consistently higher for STACEY. A random subset of 56 alignments had similar resolution to the 524-locus SNP data set. The STRUCTURE-like sparse Non-negative Matrix Factorisation (sNMF) method was applied to six individuals from each of 48 geographical populations and 28023 SNPs. Significantly fewer (13) clusters were identified as optimal by this analysis compared to the MSC methods. The sNMF clusters correspond closely to clades consistently supported by MSC methods, and showed evidence of admixture, especially in the western Cape Floristic Region. We discuss the significance of these findings, and conclude that it is important to a priori consider the kind of species one wants to identify when using genome-scale data, the assumptions behind the parametric models applied, and the potential consequences of model violations may have.

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Molecular systematics of Thouarella (Octocorallia:Primnoidae) with the description of three new species from the Southern Ocean based on combined molecular and morphological evidence

Invertebrate Systematics ◽

10.1071/is20078 ◽

2021 ◽

Author(s):

Mónica Núñez-Flores ◽

Daniel Gomez-Uchida ◽

Pablo J. López-González

Keyword(s):

New Species ◽

Southern Ocean ◽

Species Delimitation ◽

Nuclear Dna ◽

Phylogenetic Analyses ◽

Weddell Sea ◽

Morphological Evidence ◽

Three New Species ◽

Taxonomic Framework ◽

The Antarctic

Thouarella Gray, 1870, is one of the most speciose genera among gorgonians of the family Primnoidae (Cnidaria:Octocorallia:Anthozoa), being remarkably diverse in the Antarctic and sub-Antarctic seafloor. However, their diversity in the Southern Ocean is likely underestimated. Phylogenetic analyses of mitochondrial and nuclear DNA markers were integrated with species delimitation approaches as well as morphological colonial and polyps features and skeletal SEM examinations to describe and illustrate three new species within Thouarella, from the Weddell Sea, Southern Ocean: T. amundseni sp. nov., T. dolichoespinosa sp. nov. and T. pseudoislai sp. nov. Our species delimitation results suggest, for the first time, the potential presence of Antarctic and sub-Antarctic cryptic species of primnoids, based on the likely presence of sibling species within T. undulata and T. crenelata. With the three new species here described, the global diversity of Thouarella has increased to 41 species, 15 of which are endemic to the Antarctic and sub-Antarctic waters. Consequently, our results provide new steps for uncovering the shelf benthonic macrofauna’s hidden diversity in the Southern Ocean. Finally, we recommend using an integrative taxonomic framework in this group of organisms and species delimitation approaches because the distinctions between some Thouarella species based only on a superficial examination of their macro- and micromorphological features is, in many cases, limited.

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Species delimitation and population structure in three Onosma (Boraginaceae) species

Biologia ◽

10.1515/biolog-2015-0151 ◽

2015 ◽

Vol 70 (10) ◽

Author(s):

Masoud Sheidai ◽

Samira Sadeghi ◽

Mahnaz-Arab Ameri ◽

Ahmad-Reza Mehrabeian

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Species Delimitation ◽

Genetic Difference ◽

Morphological Variability ◽

Morphological Diversity ◽

Mantel Test ◽

Geographical Distance ◽

Nj Tree ◽

Issr Molecular Markers

AbstractThe present study aimed to reveal genetic diversity and population structure in three Onosma species i.e., Onosma bulbotrichum DC., O. elwendicum Wettst. and O. sericeum Willd. (Boraginaceae) growing in Iran. This study was performed to check if the ISSR molecular markers could be used in the Onosma species delimitation. We also investigated the infra-specific morphological variability and if we can identify infra-species taxonomic forms. The present study revealed within species genetic and morphological diversity. ISSR data could delimit the studied species as they were separated from each other in NJ tree, maximum parsimony and STRUCTURE analysis. AMOVA and Hickory tests produced significant genetic difference among the studied species. The Mantel test showed no correlation between genetic distance and geographical distance of the populations for all three species. Reticulation analysis and Nm estimation showed gene flow among these populations. We could identify a few ISSR loci that are adaptive. Data obtained can be used in conservation of these medicinal plants in Iran.

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Rapid ecological specialization despite constant population sizes

PeerJ ◽

10.7717/peerj.6476 ◽

2019 ◽

Vol 7 ◽

pp. e6476 ◽

Cited By ~ 1

Author(s):

Andrinajoro R. Rakotoarivelo ◽

Paul O’Donoghue ◽

Michael W. Bruford ◽

Yoshan Moodley

Keyword(s):

East Africa ◽

Nuclear Dna ◽

Incomplete Lineage Sorting ◽

Demographic History ◽

12S Rrna ◽

Surprising Result ◽

Ecological Specialization ◽

Lineage Sorting ◽

Mt Dna ◽

Data Set

Background The bushbuck, Tragelaphus scriptus, is a widespread and ecologically diverse ungulate species complex within the spiral-horned antelopes. This species was recently found to consist of two genetically divergent but monophyletic lineages, which are paraphyletic at mitochondrial (mt)DNA owing to an ancient interspecific hybridization event. The Scriptus lineage (T. s. scriptus) inhabits the north-western half of the African continent while Sylvaticus (T. s. sylvaticus) is found in the south-eastern half. Here we test hypotheses of historical demography and adaptation in bushbuck using a higher-resolution framework, with four nuclear (MGF, PRKCI, SPTBN, and THY) and three new mitochondrial markers (cytochrome b, 12S rRNA, and 16S rRNA). Methods Genealogies were reconstructed for the mitochondrial and nuclear data sets, with the latter dated using fossil calibration points. We also inferred the demographic history of Scriptus and Sylvaticus using coalescent-based methods. To obtain an overview of the origins and ancestral colonisation routes of ancestral bushbuck sequences across geographic space, we conducted discrete Bayesian phylogeographic and statistical dispersal-vicariance analyses on our nuclear DNA data set. Results Both nuclear DNA and mtDNA support previous findings of two genetically divergent Sylvaticus and Scriptus lineages. The three mtDNA loci confirmed 15 of the previously defined haplogroups, including those with convergent phenotypes. However, the nuclear tree showed less phylogenetic resolution at the more derived parts of the genealogy, possibly due to incomplete lineage sorting of the slower evolving nuclear genome. The only exception to this was the montane Menelik’s bushbuck (Sylvaticus) of the Ethiopian highlands, which formed a monophyletic group at three of four nuclear DNA loci. We dated the coalescence of the two lineages to a common ancestor ∼2.54 million years ago. Both marker sets revealed similar demographic histories of constant population size over time. We show that the bushbuck likely originated in East Africa, with Scriptus dispersing to colonise suitable habitats west of the African Rift and Sylvaticus radiating from east of the Rift into southern Africa via a series of mainly vicariance events. Discussion Despite lower levels of genetic structure at nuclear loci, we confirmed the independent evolution of the Menelik’s bushbuck relative to the phenotypically similar montane bushbuck in East Africa, adding further weight to previous suggestions of convergent evolution within the bushbuck complex. Perhaps the most surprising result of our analysis was that both Scriptus and Sylvaticus populations remained relatively constant throughout the Pleistocene, which is remarkable given that this was a period of major climatic and tectonic change in Africa, and responsible for driving the evolution of much of the continent’s extant large mammalian diversity.

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