Multilocus coalescent species delimitation reveals widespread cryptic differentiation among Drakensberg mountain-living freshwater crabs (Decapoda : Potamonautes)

2016 ◽  
Vol 30 (1) ◽  
pp. 60 ◽  
Author(s):  
Ethel Emmarantia Phiri ◽  
Savel Regan Daniels
Keyword(s):  
Species Delimitation ◽  
Species Complex ◽  
Recent Common Ancestor ◽  
12S Rrna ◽  
Mountain Range ◽  
28S Rrna ◽  
Cryptic Diversity ◽  
Most Recent Common Ancestor ◽  
Freshwater Crabs ◽  
Conservation Implications

Cryptic lineages present major challenges for evolutionary and conservation studies, particularly where these lineages remain undiscovered. Freshwater crabs are known to harbour cryptic diversity, in most cases with limited morphological differences. During the present study, we used a multilocus (12S rRNA, 16S rRNA, COI, 28S rRNA, DecapANT and PEPCK) Bayesian species delimitation to examine cryptic diversity within a freshwater crab species complex (Potamonautes clarus/P. depressus). We sampled 25 highland rivers in the Tugela and uMkomazi River drainage systems of the Drakensberg Mountain range, in the KwaZulu–Natal province of South Africa. Our results showed there to be at least eight lineages: six novel potamonautid freshwater crabs, and two described taxa P. clarus and P. depressus. Divergence from the most recent common ancestor occurred between the mid- and late Miocene (12.1 Mya), while divergence within the species complex occurred ~10.3 Mya up until the Holocene (0.11 Mya). The discovery of six novel lineages of freshwater crabs from a seemingly restricted distribution range has conservation implications, but to date most conservation planning strategies have focussed on freshwater vertebrates. By conducting a fine-scale phylogenetic survey using invertebrates, this study provides a platform for the inclusion of freshwater invertebrates in future conservation assessments.

Hidden in the highlands: the description and phylogenetic position of a novel endemic freshwater crab species (Potamonautidae : Potamonautes) from Zimbabwe

2013 ◽  
Vol 27 (5) ◽  
pp. 530 ◽  
Author(s):  
Ethel E. Phiri ◽  
Savel R. Daniels
Keyword(s):  
Southern Africa ◽  
Sequence Data ◽  
Phylogenetic Position ◽  
12S Rrna ◽  
Mountain Range ◽  
Freshwater Crab ◽  
Crab Species ◽  
Mountainous Regions ◽  
Freshwater Crabs ◽  
Mtdna Sequence

A recent sampling endeavour of freshwater crabs along the high-lying streams of the Nyanga mountain range in Mutare (Eastern Highlands, Zimbabwe) yielded a morphologically distinct, as yet undescribed species. The novel Zimbabwean species is compared to the 16 described species from southern Africa based on mtDNA sequence data derived from three partial gene sequences (12S rRNA, 16S rRNA and COI). The new Zimbabwean species was found to be a sister taxon to Potamonautes mulanjeensis. These two species are morphologically and genetically easily differentiated. The new species is described as Potamonautes mutareensis, sp. nov. and is compared morphologically to the known freshwater crab species of southern Africa. A dichotomous key to the four described freshwater crab species that occur in Zimbabwe is also provided. Our results suggest that species diversity and endemism of freshwater decapods and other habitat specialists is likely to be high in unsampled mountainous regions.

Phylogenetic origin of the Monotropoideae inferred from partial 28S ribosomal RNA gene sequences

1992 ◽  
Vol 70 (8) ◽  
pp. 1703-1708 ◽  
Author(s):  
K. W. Cullings ◽  
T. D. Bruns
Keyword(s):  
Ribosomal Rna ◽  
Recent Common Ancestor ◽  
Gradual Transition ◽  
Rrna Gene ◽  
28S Rrna ◽  
28S Rrna Gene ◽  
Most Recent Common Ancestor ◽  
Alternative Hypotheses ◽  
Degree Of Confidence ◽  
Phylogenetic Origin

Despite more than 100 years of detailed analysis of morphology and macromolecules, the phylogenetic origin of the Monotropoideae remains unclear. In this study partial sequences from the 28S rRNA gene were used to test two alternative hypotheses: (i) that the Monotropoideae share a most recent common ancestor with the Arbutoideae in the Ericaceae or (ii) that the Monotropoideae is the end result of a gradual transition from autotrophism to mycotrophic parasitism in the Pyrolaceae. Our results support the hypothesis that the Monotropoideae and the Arbutoideae are a monophyletic group and that the Monotropoideae should be included in the Ericaceae rather than the Pyrolaceae. The Monotropoid species Pleuricospora fimbriolata could not be placed within either the Monotropoideae or the Arbutoideae with any degree of confidence, leaving open the possibility that the Monotropoideae is polyphyletic. Key words: Monotropoideae, Ericaceae, 28S rRNA gene, PCR, molecular systematics.

scholarly journals Rapid evolution of troglomorphic characters suggests selection rather than neutral mutation as a driver of eye reduction in cave crabs

2013 ◽  
Vol 9 (2) ◽  
pp. 20121098 ◽  
Author(s):  
Sebastian Klaus ◽  
José C. E. Mendoza ◽  
Jia Huan Liew ◽  
Martin Plath ◽  
Rudolf Meier ◽  
...  
Keyword(s):  
Temporal Pattern ◽  
Common Ancestor ◽  
Rapid Evolution ◽  
Genetic Distances ◽  
Directional Selection ◽  
Neutral Evolution ◽  
Recent Common Ancestor ◽  
Mitochondrial Markers ◽  
Most Recent Common Ancestor ◽  
Freshwater Crabs

This study asked whether reductive traits in cave organisms evolve at a slower pace (suggesting neutral evolution under relaxed selection) than constructive changes, which are likely to evolve under directional selection. We investigated 11 subterranean and seven surface populations of Sundathelphusa freshwater crabs on Bohol Island, Philippines, and examined constructive traits associated with improved food finding in darkness (increased leg and setae length) and reductive traits (reduced cornea size and eyestalk length). All changes occurred rapidly, given that the age of the most recent common ancestor was estimated to be 722–271 ka based on three mitochondrial markers. In order to quantify the speed of character change, we correlated the degree of morphological change with genetic distances between surface and subterranean individuals. The temporal pattern of character change following the transition to subterranean life was indistinguishable for constructive and reductive traits, characterized by an immediate onset and rapid evolutionary change. We propose that the evolution of these reductive traits—just like constructive traits—is most likely driven by strong directional selection.

scholarly journals Serpentine mountain uplift in northern Japan triggered the divergence of a narrow endemic from a widespread (sub)arctic Asia-Alaska species complex of Lagotis (Plantaginaceae)

2019 ◽  
Author(s):  
Atsushi Sugano ◽  
Tomoko Fukuda ◽  
Yoshinori Murai ◽  
Olga A Chernyagina ◽  
Suyama Yoshihisa ◽  
...  
Keyword(s):  
Species Complex ◽  
Incomplete Lineage Sorting ◽  
Nuclear Gene ◽  
Volcanic Eruptions ◽  
Early Pleistocene ◽  
Recent Common Ancestor ◽  
Widespread Species ◽  
Most Recent Common Ancestor ◽  
Narrow Endemics ◽  
Northern Japan

AbstractIn the circumboreal region, plants often have extremely-wide species ranges. Lagotis minor-glauca species complex widespread from (sub)arctic Asia to Alaska, however, have two allied narrow endemics in northern Japan: a serpentine plant L. takedana endemic to the Yubari Mountains (Mt. Yubari) and a non-serpentine plant L. yesoensis endemic to the Taisetsu Mountains (Mt. Taisetsu). Elucidating their origins sheds light on drivers for secondary-speciation of widespread circumboreal plants. To infer phylogenetic distinctiveness of two narrow endemics with those related taxa, which contained 25 out of all the 29 species of the genus, chloroplast DNA (cpDNA), nuclear ribosomal (nrITS), two low copy nuclear gene (LCN) markers and genome-wide single-nucleotide polymorphism genotyping (MIG-seq) were used. In the result of cpDNA analyses, the Lagotis minor-glauca species complex formed a clade. Within the clade, L. yesoensis and a portion of L. glauca samples formed a subclade. However, monophyly of each of the four species was not supported. In the results of nrITS and two LCN analyses, L. takedana was monophyletic, while monophyly was not recovered for each L. yesoensis, L. glauca, and L. minor. Based on a Bayesian dating analysis using nrITS data, the age of the most recent common ancestor of L. takedana was Ma (95% confidence interval: 0.05-1.75 Ma). Possible scenario is that an ancestral linage being adapted to serpentine soils migrated into the alpine habitat of Mt. Yubari, that was formed with mountain uplift by the early Pleistocene, and subsequently reproductively isolated from non-serpentine populations and speciated. The contrasting result of L. yesoensis, that was phylogenetically indistinct, is possibly explained by incorrect taxonomy, or alternatively, shallow history and incomplete lineage sorting. In Mt. Taisetsu, massive volcanic eruptions had occurred the Early Pleistocene and even after the last glacial period, suggesting that alpine plants have not migrated into and established populations in Mt. Taisetsu until very recently. To fully resolve the phylogeny of the three species L. yesoensis, L. glauca, and L. minor, further analyses using high resolution molecular markers are needed. The present study illustrated that two narrow endemics in northern Japan diverged from the widespread species include phylogenetically distinctive and indistinctive species, owing to historical orogeny and ecological factors.

scholarly journals The probability of monophyly of a sample of gene lineages on a species tree

2016 ◽  
Vol 113 (29) ◽  
pp. 8002-8009 ◽  
Author(s):  
Rohan S. Mehta ◽  
David Bryant ◽  
Noah A. Rosenberg
Keyword(s):  
Species Delimitation ◽  
Common Ancestor ◽  
Species Group ◽  
Species Tree ◽  
Recent Common Ancestor ◽  
Evolutionary Models ◽  
Tree Model ◽  
Most Recent Common Ancestor ◽  
Branch Lengths ◽  
Multiple Species

Monophyletic groups—groups that consist of all of the descendants of a most recent common ancestor—arise naturally as a consequence of descent processes that result in meaningful distinctions between organisms. Aspects of monophyly are therefore central to fields that examine and use genealogical descent. In particular, studies in conservation genetics, phylogeography, population genetics, species delimitation, and systematics can all make use of mathematical predictions under evolutionary models about features of monophyly. One important calculation, the probability that a set of gene lineages is monophyletic under a two-species neutral coalescent model, has been used in many studies. Here, we extend this calculation for a species tree model that contains arbitrarily many species. We study the effects of species tree topology and branch lengths on the monophyly probability. These analyses reveal new behavior, including the maintenance of nontrivial monophyly probabilities for gene lineage samples that span multiple species and even for lineages that do not derive from a monophyletic species group. We illustrate the mathematical results using an example application to data from maize and teosinte.

Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex

2020 ◽  
Vol 29 (12) ◽  
pp. 2269-2287 ◽  
Author(s):  
Lacie G. Newton ◽  
James Starrett ◽  
Brent E. Hendrixson ◽  
Shahan Derkarabetian ◽  
Jason E. Bond
Keyword(s):  
Species Delimitation ◽  
Species Complex ◽  
Cryptic Diversity ◽  
Southern Appalachian

scholarly journals Allelic Genealogies in Sporophytic Self-Incompatibility Systems in Plants

Genetics ◽  
1998 ◽  
Vol 150 (3) ◽  
pp. 1187-1198 ◽  
Author(s):  
Mikkel H Schierup ◽  
Xavier Vekemans ◽  
Freddy B Christiansen
Keyword(s):  
Dominance Hierarchy ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Self Incompatibility ◽  
Most Recent Common Ancestor ◽  
Dominance Interactions ◽  
Turnover Process ◽  
Neutral Gene ◽  
Interspecific Comparisons ◽  
Coalescence Times

Abstract Expectations for the time scale and structure of allelic genealogies in finite populations are formed under three models of sporophytic self-incompatibility. The models differ in the dominance interactions among the alleles that determine the self-incompatibility phenotype: In the SSIcod model, alleles act codominantly in both pollen and style, in the SSIdom model, alleles form a dominance hierarchy, and in SSIdomcod, alleles are codominant in the style and show a dominance hierarchy in the pollen. Coalescence times of alleles rarely differ more than threefold from those under gametophytic self-incompatibility, and transspecific polymorphism is therefore expected to be equally common. The previously reported directional turnover process of alleles in the SSIdomcod model results in coalescence times lower and substitution rates higher than those in the other models. The SSIdom model assumes strong asymmetries in allelic action, and the most recessive extant allele is likely to be the most recent common ancestor. Despite these asymmetries, the expected shape of the allele genealogies does not deviate markedly from the shape of a neutral gene genealogy. The application of the results to sequence surveys of alleles, including interspecific comparisons, is discussed.

scholarly journals Molecular epidemiological characteristics of echovirus 6 in mainland China: extensive circulation of genotype F from 2007 to 2018

2021 ◽  
Author(s):  
Wenjun Cheng ◽  
Tianjiao Ji ◽  
Shuaifeng Zhou ◽  
Yong Shi ◽  
Lili Jiang ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Mainland China ◽  
Recent Common Ancestor ◽  
Genetic Characteristics ◽  
Most Recent Common Ancestor ◽  
Significant Difference ◽  
Echovirus 6 ◽  
Epidemiological Characteristics ◽  
Highest Posterior Density ◽  
Genotype F

AbstractEchovirus 6 (E6) is associated with various clinical diseases and is frequently detected in environmental sewage. Despite its high prevalence in humans and the environment, little is known about its molecular phylogeography in mainland China. In this study, 114 of 21,539 (0.53%) clinical specimens from hand, foot, and mouth disease (HFMD) cases collected between 2007 and 2018 were positive for E6. The complete VP1 sequences of 87 representative E6 strains, including 24 strains from this study, were used to investigate the evolutionary genetic characteristics and geographical spread of E6 strains. Phylogenetic analysis based on VP1 nucleotide sequence divergence showed that, globally, E6 strains can be grouped into six genotypes, designated A to F. Chinese E6 strains collected between 1988 and 2018 were found to belong to genotypes C, E, and F, with genotype F being predominant from 2007 to 2018. There was no significant difference in the geographical distribution of each genotype. The evolutionary rate of E6 was estimated to be 3.631 × 10-3 substitutions site-1 year-1 (95% highest posterior density [HPD]: 3.2406 × 10-3-4.031 × 10-3 substitutions site-1 year-1) by Bayesian MCMC analysis. The most recent common ancestor of the E6 genotypes was traced back to 1863, whereas their common ancestor in China was traced back to around 1962. A small genetic shift was detected in the Chinese E6 population size in 2009 according to Bayesian skyline analysis, which indicated that there might have been an epidemic around that year.

scholarly journals Molecular epidemiology of coxsackievirus A16 circulating in children in Beijing, China from 2010 to 2019

2021 ◽  
Author(s):  
Ya-Fang Hu ◽  
Li-Ping Jia ◽  
Fang-Yuan Yu ◽  
Li-Ying Liu ◽  
Qin-Wei Song ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Evolutionary Rate ◽  
Foot And Mouth Disease ◽  
Recent Common Ancestor ◽  
Rt Pcr ◽  
Coxsackievirus A16 ◽  
Most Recent Common Ancestor ◽  
Etiological Agents ◽  
High Level ◽  
And Control

Abstract Background Coxsackievirus A16 (CVA16) is one of the major etiological agents of hand, foot and mouth disease (HFMD). This study aimed to investigate the molecular epidemiology and evolutionary characteristics of CVA16. Methods Throat swabs were collected from children with HFMD and suspected HFMD during 2010–2019. Enteroviruses (EVs) were detected and typed by real-time reverse transcription-polymerase chain reaction (RT-PCR) and RT-PCR. The genotype, evolutionary rate, the most recent common ancestor, population dynamics and selection pressure of CVA16 were analyzed based on viral protein gene (VP1) by bioinformatics software. Results A total of 4709 throat swabs were screened. EVs were detected in 3180 samples and 814 were CVA16 positive. More than 81% of CVA16-positive children were under 5 years old. The prevalence of CVA16 showed obvious periodic fluctuations with a high level during 2010–2012 followed by an apparent decline during 2013–2017. However, the activities of CVA16 increased gradually during 2018–2019. All the Beijing CVA16 strains belonged to sub-genotype B1, and B1b was the dominant strain. One B1c strain was detected in Beijing for the first time in 2016. The estimated mean evolutionary rate of VP1 gene was 4.49 × 10–3 substitution/site/year. Methionine gradually fixed at site-23 of VP1 since 2012. Two sites were detected under episodic positive selection, one of which (site-223) located in neutralizing linear epitope PEP71. Conclusions The dominant strains of CVA16 belonged to clade B1b and evolved in a fast evolutionary rate during 2010–2019 in Beijing. To provide more favorable data for HFMD prevention and control, it is necessary to keep attention on molecular epidemiological and evolutionary characteristics of CVA16.

scholarly journals The Ancestry of a Sample of Sequences Subject to Recombination

Genetics ◽  
1999 ◽  
Vol 151 (3) ◽  
pp. 1217-1228 ◽  
Author(s):  
Carsten Wiuf ◽  
Jotun Hein
Keyword(s):  
Genetic Distance ◽  
Population Size ◽  
Upper Bound ◽  
Recombination Rate ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Sequence Length ◽  
Most Recent Common Ancestor ◽  
The Mean ◽  
Mean Time

Abstract In this article we discuss the ancestry of sequences sampled from the coalescent with recombination with constant population size 2N. We have studied a number of variables based on simulations of sample histories, and some analytical results are derived. Consider the leftmost nucleotide in the sequences. We show that the number of nucleotides sharing a most recent common ancestor (MRCA) with the leftmost nucleotide is ≈log(1 + 4N Lr)/4Nr when two sequences are compared, where L denotes sequence length in nucleotides, and r the recombination rate between any two neighboring nucleotides per generation. For larger samples, the number of nucleotides sharing MRCA with the leftmost nucleotide decreases and becomes almost independent of 4N Lr. Further, we show that a segment of the sequences sharing a MRCA consists in mean of 3/8Nr nucleotides, when two sequences are compared, and that this decreases toward 1/4Nr nucleotides when the whole population is sampled. A measure of the correlation between the genealogies of two nucleotides on two sequences is introduced. We show analytically that even when the nucleotides are separated by a large genetic distance, but share MRCA, the genealogies will show only little correlation. This is surprising, because the time until the two nucleotides shared MRCA is reciprocal to the genetic distance. Using simulations, the mean time until all positions in the sample have found a MRCA increases logarithmically with increasing sequence length and is considerably lower than a theoretically predicted upper bound. On the basis of simulations, it turns out that important properties of the coalescent with recombinations of the whole population are reflected in the properties of a sample of low size.

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