scholarly journals Molecular Phylogeny and Phylogeography of Potentilla multifida L. agg. (Rosaceae) in Northern Eurasia with Special Focus on Two Rare and Critically Endangered Endemic Species, P. volgarica and P. eversmanniana

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1798
Author(s):  
Ivan A. Schanzer ◽  
Alina V. Fedorova ◽  
Olga V. Shelepova ◽  
Guzyaliya F. Suleymanova

The results of a molecular genetic study of Potentilla multifida agg. using two plastid markers (ndhC-trnV and psbA-trnH) and a nuclear ITS marker suggested that this group comprises a number of relatively young and incompletely differentiated species widely distributed in Northern Eurasia. The sequences were analyzed using tree-based (maximum likelihood) and network-based (statistical parsimony network) approaches. The plastid data suggested incomplete lineage sorting, characteristic of the group as a whole. The nuclear ITS results demonstrated quite a different pattern, with mostly conspecific accessions shaping monophyletic clades. The majority of the Potentilla sect. Multifidae species studied possess few, usually closely related plastid haplotypes, or are even monomorphic. In contrast, P. volgarica, a narrow endemic from the Volga River valley, presents plastid haplotypes belonging to two distantly related groups. Such a pattern of genetic diversity in P. volgarica may be explained by a long persistence of the species within an extremely small distribution range, on the right bank of the Volga River, most likely representing a contemporary refugium. The genealogy of plastid markers in P. volgarica suggests that this species is ancestral to P.eversmanniana, another narrow endemic from the S Urals.

2020 ◽  
Vol 24 (4) ◽  
pp. 420-426
Author(s):  
A. A. Poroshina ◽  
D. Y. Sherbakov ◽  
T. E. Peretolchina

In ancient freshwater lakes, an abnormally large species diversity is observed. The mechanisms that g nerated extremely high biodiversity in the ancient lakes have not been sufficiently studied and remain only partially known. Sequences of environmental changes in highly complex ecosystems such as Lake Baikal, may induce sophisticated combinations of microevolutionary processes. These processes are likely to result in unusual “patterns” of genetic variability of species. The most unusual patterns include the ones when speciation is followed by incomplete lineage sorting as well as mitochondrial or nuclear introgression. All these phenomena are diagnosed by comparing the topologies of phylogenetic trees inferred from molecular markers of evolution located in mitochondria and nuclei. Mitochondrial and nuclear introgression is a particularly interesting and complex case, which is the process of incorporating the gene alleles of one species into the gene pool of a sister species due to interspecific hybridization (introgressive hybridization). In many cases, existing methods for molecular phylogenetic analysis do not automatically allow the observed patterns of polymorphism to be explained and, therefore, cannot provide hypotheses that would explain the mechanisms which resulted to these patterns. Here we use adaptive dynamics models to study neutral molecular evolution under various scenarios of interaction between sister species and the environment. We propose and justify a set of criteria for detecting how two evolutionary trees may differ, with a special focus on comparing a tree inferred from nuclear DNA to one from mitochondrial DNA. The criteria react to branching pattern and branch lengths, including relative distances from ancestral lineages. Simulations show that the criteria allow fast and automated detection of various types of introgression, secondary breaches of reproductive barriers, and incomplete lineage sorting.


2020 ◽  
Vol 195 (1) ◽  
pp. 53-76
Author(s):  
Ronaldo Vinícius-Silva ◽  
Lynn G Clark ◽  
Jéferson Nunes Fregonezi ◽  
Ana Paula Santos-Gonçalves

Abstract Merostachys is a Neotropical woody bamboo genus that occurs in the understory and along forest borders. Our taxonomic studies of its species and morphological analyses have allowed us to recognize morphological groups in the genus. Previous molecular analyses, which included relatively few species, supported Merostachys as monophyletic and sister to Actinocladum or Athroostachys. We here provide a phylogenetic estimation for Merostachys based on a broader taxon sampling and seven plastid markers (one coding: ndhF 3′ end; four intergenic spacers: rps16-trnQ, trnC-rpoB, trnD-trnT and trnT-trnL; and two introns: rpl16 and rps16). We aimed to test the monophyly of the genus, to verify its relationship with other genera of Arthrostylidiinae, mainly Athroostachys and Actinocladum, and to test whether the previously identified morphological groups were congruent with the molecular data. The monophyly of the genus was confirmed, as was its sister relationship with Athroostachys, although alternate hypothesis testing could not reject a sister relationship with Actinocladum. Two well-supported clades in Merostachys were recovered, one of which encompasses a polytomy. These clades did not exhibit consistent morphological synapomorphies and were not congruent with the morphological groups; however, floret surface (shiny vs. dull) was correlated with the two clades. The lack of resolution in Merostachys, as exemplified by the polytomy, can be attributed mainly to incomplete lineage sorting, suggesting a recent radiation in this group.


The Auk ◽  
2003 ◽  
Vol 120 (3) ◽  
pp. 889-907
Author(s):  
Kim T. Scribner ◽  
Sandra L. Talbot ◽  
John M. Pearce ◽  
Barbara J. Pierson ◽  
Karen S. Bollinger ◽  
...  

Abstract Using molecular genetic markers that differ in mode of inheritance and rate of evolution, we examined levels and partitioning of genetic variation for seven nominal subspecies (11 breeding populations) of Canada Geese (Branta canadensis) in western North America. Gene trees constructed from mtDNA control region sequence data show that subspecies of Canada Geese do not have distinct mtDNA. Large and small-bodied forms of Canada Geese were highly diverged (0.077 average sequence divergence) and represent monophyletic groups. A majority (65%) of 20 haplotypes resolved were observed in single breeding locales. However, within both large and small-bodied forms certain haplotypes occurred across multiple subspecies. Population trees for both nuclear (microsatellites) and mitochondrial markers were generally concordant and provide resolution of population and subspecific relationships indicating incomplete lineage sorting. All populations and subspecies were genetically diverged, but to varying degrees. Analyses of molecular variance, nested-clade and coalescencebased analyses of mtDNA suggest that both historical (past fragmentation) and contemporary forces have been important in shaping current spatial genetic distributions. Gene flow appears to be ongoing though at different rates, even among currently recognized subspecies. The efficacy of current subspecific taxonomy is discussed in light of hypothesized historical vicariance and current demographic trends of management and conservation concern.


2008 ◽  
Vol 21 (4) ◽  
pp. 229 ◽  
Author(s):  
Cornelia Löhne ◽  
Thomas Borsch ◽  
Surrey W. L. Jacobs ◽  
C. Barre Hellquist ◽  
John H. Wiersema

This study represents the first comprehensive analysis of phylogenetic relationships within the Australian water-lilies, Nymphaea subg. Anecphya. Our 51-accession dataset covers all 10 species of the subgenus, except the newly described N. alexii, and includes information from the nuclear ITS as well as from the chloroplast trnT–trnF region. The results show that molecular data are consistent with morphology, because the subdivision of subg. Anecphya into two major clades, a large-seeded and a small-seeded group, could be confirmed. Within the large-seeded group, Nymphaea atrans and N. immutabilis seem to form one clade, whereas samples of N. gigantea, N. georginae, N. macrosperma and N. carpentariae form another. Relationships within the small-seeded group, containing all samples of N. violacea, N. elleniae and N. hastifolia, are less clear, since the trees obtained from the chloroplast and the nuclear marker are incongruent. The samples of N. violacea do not form a monophyletic group in each of the trees, but—at least in the ITS tree—group with either N. elleniae or N. hastifolia/Ondinea, respectively. Polymorphisms among ITS paralogues, i.e. substitutions at single nucleotide positions and length polymorphisms, have been observed in some samples of N. violacea. This fact as well as the incongruent phylogenetic signal obtained from the chloroplast and the nuclear genomes point to recent hybridisation or introgression in this group. Remarkably, Ondinea purpurea is resolved within the small-seeded group by both markers and seems to have a close relationship to N. hastifolia. Although incomplete lineage sorting cannot be fully excluded to explain high variability in N. violacea, molecular data potentially hint to a case of still imperfect taxonomy.


2020 ◽  
Vol 98 (3) ◽  
pp. 218-225
Author(s):  
J. A. Krupinova ◽  
N. G. Mokrysheva ◽  
N. Y. Kalinchenko ◽  
A. K. Eremkina ◽  
A. N. Polyakov ◽  
...  

Multiple endocrine neoplasia type 1 (MEN-1) is the most common cause of the hereditary type of primary hyperparathyroidism (PHPT). If a family type of PHPT is suspected, a dynamic monitoring of patients and their close relatives should be carried out throughout their lives. We present a clinical case of a family in which four members of a pedigree were diagnosed with familial isolated hyperparathyroidism (FIHP). The diagnosis was changed to MEN-1, because it appeared that one of the patients had pancreatic neuroendocrine tumor. Molecular genetic study of MEN1 by direct by means of Sanger sequencing revealed that six family members had a new heterozygous mutation in exon 9: s. 1252 G> T p. D418Y.


2020 ◽  
Author(s):  
Liming Cai ◽  
Zhenxiang Xi ◽  
Emily Moriarty Lemmon ◽  
Alan R Lemmon ◽  
Austin Mast ◽  
...  

Abstract The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes nine of the top ten most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 10.0%, 34.8%, and 21.4% of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution.


Insects ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 455
Author(s):  
Na Ra Jeong ◽  
Min Jee Kim ◽  
Sung-Soo Kim ◽  
Sei-Woong Choi ◽  
Iksoo Kim

Conogethes pinicolalis has long been considered as a Pinaceae-feeding type of the yellow peach moth, C. punctiferalis, in Korea. In this study, the divergence of C. pinicolalis from the fruit-feeding moth C. punctiferalis was analyzed in terms of morphology, ecology, and genetics. C. pinicolalis differs from C. punctiferalis in several morphological features. Through field observation, we confirmed that pine trees are the host plants for the first generation of C. pinicolalis larvae, in contrast to fruit-feeding C. punctiferalis larvae. We successfully reared C. pinicolalis larvae to adults by providing them pine needles as a diet. From a genetic perspective, the sequences of mitochondrial COI of these two species substantially diverged by an average of 5.46%; moreover, phylogenetic analysis clearly assigned each species to an independent clade. On the other hand, nuclear EF1α showed a lower sequence divergence (2.10%) than COI. Overall, EF1α-based phylogenetic analysis confirmed each species as an independent clade, but a few haplotypes of EF1α indicated incomplete lineage sorting between these two species. In conclusion, our results demonstrate that C. pinicolalis is an independent species according to general taxonomic criteria; however, analysis of the EF1α sequence revealed a short divergence time.


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