scholarly journals Some Examples of the Use of Molecular Markers for Needs of Basic Biology and Modern Society

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1473
Author(s):  
Yuri Phedorovich Kartavtsev
Keyword(s):  
Meta Analysis ◽  
Molecular Genetic ◽  
Modern Society ◽  
Molecular Data ◽  
Biological Species ◽  
Social Needs ◽  
Biological Species Concept ◽  
Genetic Introgression ◽  
Gene Trees ◽  
Modern Biology

Application of molecular genetic markers appeared to be very fruitful in achieving many goals, including (i) proving the theoretic basements of general biology and (ii) assessment of worldwide biodiversity. Both are provided in the present meta-analysis and a review as the main signal. One of the basic current challenges in modern biology in the face of new demands in the 21st century is the validation of its paradigms such as the synthetic theory of evolution (STE) and biological species concept (BSC). Another of most valuable goals is the biodiversity assessment for a variety of social needs including free web-based information resources about any living being, renovation of museum collections, nature conservation that recognized as a global project, iBOL, as well as resolving global trading problems such as false labeling of species specimens used as food, drug components, entertainment, etc. The main issues of the review are focused on animals and combine four items. (1) A combination of nDNA and mtDNA markers best suits the identification of hybrids and estimation of genetic introgression. (2) The available facts on nDNA and mtDNA diversity seemingly make introgression among many taxa obvious, although it is evident, that introgression may be quite restricted or asymmetric, thus, leaving at least the “source” taxon (taxa) intact. (3) If we consider sexually reproducing species in marine and terrestrial realms introgressed, as it is still evident in many cases, then we should recognize that the BSC, in view of the complete lack of gene flow among species, is inadequate because many zoological species are not biological ones yet. However, vast modern molecular data have proven that sooner or later they definitely become biological species. (4) An investigation into the fish taxa divergence using the BOLD database shows that most gene trees are basically monophyletic and interspecies reticulations are quite rare.

Fern nothogenera and ×Lepinema, a new hybrid genus between Ellipinema and Lepisorus (Polypodiaceae)

Phytotaxa ◽  
2020 ◽  
Vol 455 (4) ◽  
pp. 262-266
Author(s):  
LIANG ZHANG ◽  
LI-BING ZHANG
Keyword(s):  
Species Concept ◽  
Intergeneric Hybrid ◽  
Molecular Data ◽  
Biological Species ◽  
Biological Species Concept

The biological species concept is not exclusively applicable in many groups of organisms including ferns. Interspecific fern hybrids are not rare: there are 16 intergeneric hybrid genera in ferns confirmed with molecular data. Here we add one more hybrid genus in the tribe Lepisoreae of Polypodiaceae, ×Lepinema, formed via hybridization between parents in two genera: Ellipinema and Lepisorus.

Species limits in Pteruthius (Aves: Corvida) shrike-babblers: a comparison between the Biological and Phylogenetic Species Concepts

Zootaxa ◽  
2009 ◽  
Vol 2301 (1) ◽  
pp. 29-54 ◽  
Author(s):  
FRANK E. RHEINDT ◽  
JAMES A. EATON
Keyword(s):  
Species Concept ◽  
Molecular Data ◽  
Biological Species ◽  
Species Concepts ◽  
Biological Species Concept ◽  
Phylogenetic Species ◽  
Species Status ◽  
Phylogenetic Species Concept ◽  
Sampling Regime ◽  
Morphological And Molecular Data

The question of how to define a species continues to divide biologists. Meanwhile, the application of different species concepts has led to disparate taxonomic treatments that confound conservationists and other biologists. The most widely followed guidelines to species designation in avian and other vertebrate taxonomy are Ernst Mayr’s Biological Species Concept (BSC) and Joel Cracraft’s version of the Phylogenetic Species Concept (PSC). Although the BSC is considered to be more conservative in its assignment of species status, there is a lack of research demonstrating differences in taxonomic treatment between the BSC and the PSC with reference to a multi-taxon multi-trait study system. We examined the case of five traditionally recognized species of shrike-babbler (Pteruthius) that have recently been divided into 19 species under the PSC. Re-analyzing previous morphological and molecular data and adding new vocal data, we propose a BSC classification of 9 species. However, taking into consideration geographic gaps in the sampling regime, we contend that additional data will likely reduce discrepancies between the total numbers of species designated under the PSC and BSC. The current PSC species total is a likely overestimate owing to species diagnosis based on characters that erroneously appear to be unique to a taxon at low sample size. The current BSC species total as here proposed is a likely underestimate on account of the conservative designation of taxa as subspecies in equivocal cases, e.g. where BSC species status is potentially warranted but may be masked by insufficient data.

A revision of the Trimeresurus puniceus-complex (Serpentes: Viperidae: Crotalinae) based on morphological and molecular data

Zootaxa ◽  
2006 ◽  
Vol 1293 (1) ◽  
pp. 1 ◽  
Author(s):  
PATRICK DAVID ◽  
GERNOT VOGEL ◽  
S. P. VIJAYAKUMAR ◽  
NICOLAS VIDAL
Keyword(s):  
Species Concept ◽  
Distinct Species ◽  
Morphological Characters ◽  
Molecular Data ◽  
Biological Species ◽  
Valid Species ◽  
Biological Species Concept ◽  
Phylogenetic Species Concept ◽  
Morphological And Molecular Data ◽  
A New Species

The brown Asian pitvipers of the genus Trimeresurus related to Trimeresurus puniceus (informal Trimeresurus puniceus-complex) are revised on the basis of morphological and molecular analyses. Variation in morphological characters were investigated among 119 specimens from 62 populations of the whole range of the pitvipers currently known as Trimeresurus puniceus (Boie, 1827), Trimeresurus borneensis (Peters, 1872) and Trimeresurus brongersmai Hoge, 1969. Molecular and morphological analyses clearly differentiate two groups of taxa, referrable to the informal Trimeresurus puniceus-group and Trimeresurus borneensis-group, and confirm the distinct specific status of T. puniceus and T. borneensis. Morphological univariate and multivariate analyses differentiate six clusters of populations that are morphologically diagnosable, of which five are here considered to represent independent lineages and one is placed incertae sedis pending the availability of further specimens. These clusters are considered to be distinct species following the Biological Species Concept and the Phylogenetic Species Concept. One of them is described as a new species, Trimeresurus andalasensis spec. nov. (T. borneensis-group), which includes populations from northern Sumatra. Trimeresurus wiroti Trutnau, 1981 is revalidated to accommodate populations from Thailand and West Malaysia. Trimeresurus borneensis is here considered endemic to Borneo. Trimeresurus puniceus is known from Java and from South Sumatra, but the taxonomy of this species in Sumatra is left unresolved. Also left unresolved is the taxonomic position of specimens from western Sumatra and the Mentawai Archipelago, and from the Natuna Islands and Anamba Islands. Although belonging to the T. puniceus-group, they show some differences to other specimens of the group. They are not referred to any taxon pending the collection of additional specimens. Lastly, Trimeresurus brongersmai is confirmed as a valid species from the Mentawai Archipelago. A key to these taxa is provided.

Osteology in the Cuora galbinifrons complex suggests conspecifity of C. bourreti and C. galbinifrons, with notes on shell osteology and phalangeal formulae within the Geoemydidae

2006 ◽  
Vol 27 (2) ◽  
pp. 195-205 ◽  
Author(s):  
Uwe Fritz ◽  
Markus Auer ◽  
Antje Petzold
Keyword(s):  
Hainan Island ◽  
Biological Species ◽  
Shell Shape ◽  
Biological Species Concept ◽  
Character State ◽  
Genetic Introgression ◽  
X Rays ◽  
Part C ◽  
Fourth Finger ◽  
Phalangeal Formula

AbstractThirty-six complete skeletons, three shells, and x-rays of the extremities of 32 additional turtles of the Cuora galbinifrons complex have been compared with 38 other geoemydid species from 19 genera. Cuora bourreti differs from C. galbinifrons and C. picturata by a lost phalanx in the fourth finger and fourth toe. Individuals with a shell shape intermediate between C. bourreti and C. galbinifrons, as found on Hainan Island (China), have either the reduced phalangeal formula of C. bourreti (manus: 2-3-3-2-2, pes: 2-3-3-2-1) or the complete number of phalanges (manus: 2-3-3-3-2, pes: 2-3-3-3-1). Only in C. flavomarginata did we also register a lost phalanx in the fourth digit of manus and pes; in the pes of C. mouhotii the same character state may occur. In C. flavomarginata the fifth digit of the pes is also lacking. Some other terrestrial and semiterrestrial geoemydids (Cuora mccordi, Heosemys spinosa, and in part C. mouhotii and Leucocephalon yuwonoi) display a similar pattern of phalangeal reduction, resulting in the loss of the fifth digit of the pes. Likewise, in tortoises (Testudinidae), a further group of terrestrial chelonians, and the terrestrial turtle genus Terrapene (Emydidae) the loss of phalanges or complete digits is known to occur. Malayemys subtrijuga, Morenia petersi, Pangshura smithii and Siebenrockiella crassicollis differ from all other studied geoemydid taxa by an additional phalanx in the fifth digit of the manus (2-3-3-3-3); one P. smithii has on one body side three phalanges in the fifth digit of the pes (2-3-3-3-3). These are highly aquatic turtles with extensive toe webbing. Probably, longer digits (and thus a higher phalangeal number) are a favorable prerequisite for swimming while phalangeal loss seems to be the consequence of walking.Cuora bourreti and C. picturata have consistently in the bony carapace a very rare character state regarding the articulation of the rib tips with the peripheral plates. In both species the rib tips are intercalated between two peripheral plates in the bridge region. Intercalated rib tips like those in C. bourreti and C. picturata were found only in C. m. mouhotii, but not in the southern subspecies C. mouhotii obsti. In C. galbinifrons and all other geoemydid taxa studied the rib tips articulate on the bridge within the underlying peripheral and not between two peripherals. In turtles morphologically intermediate between C. bourreti and C. galbinifrons both characters states are found. This suggests that such individuals are hybrids or intergrades. Three known-locality specimens from Hainan Island display both extremes and an intermediate character state. This, together with external morphology and the occurrence of both phalangeal formulae in approximately the same frequency on that island, argues for genetic introgression of C. bourreti on the Hainan population of C. galbinifrons. We conclude that our findings qualify C. galbinifrons and C. bourreti under the Biological Species Concept as conspecific.

Biogeography and taxonomy of racket-tail hummingbirds (Aves: Trochilidae: Ocreatus): evidence for species delimitation from morphology and display behavior

Zootaxa ◽  
2016 ◽  
Vol 4200 (1) ◽  
pp. 83 ◽  
Author(s):  
KARL-L. SCHUCHMANN ◽  
ANDRÉ-A. WELLER ◽  
DIETMAR JÜRGENS
Keyword(s):  
Geographic Variation ◽  
Endemic Species ◽  
Species Delimitation ◽  
Evolutionary History ◽  
Species Concept ◽  
Molecular Data ◽  
Biological Species ◽  
Biological Species Concept ◽  
Taxonomic History ◽  
History Of

We analyzed geographic variation, biogeography, and intrageneric relationships of racket-tail hummingbirds Ocreatus (Aves, Trochilidae). Presently, the genus is usually considered monospecific, with O. underwoodii including eight subspecies (polystictus, discifer, underwoodii, incommodus, melanantherus, peruanus, annae, addae), although up to three species have been recognized by some authors. In order to evaluate the current taxonomy we studied geographic variation in coloration, mensural characters, and behavioral data of all Ocreatus taxa. We briefly review the taxonomic history of the genus. Applying the Biological Species Concept, species delimitation was based on a qualitative-quantitative criteria analysis including an evaluation of character states. Our results indicate that the genus should be considered a superspecies with four species, the monotypic Ocreatus addae, O. annae, and O. peruanus, and the polytypic O. underwoodii (including the subspecies underwoodii, discifer, incommodus, melanantherus, polystictus). In this taxonomic treatment, O. annae becomes an endemic species to Peru and O. addae is endemic to Bolivia. We recommend additional sampling of distributional, ethological, and molecular data for an improved resolution of the evolutionary history of Ocreatus. 

scholarly journals A Microsatellite Genotyping-Based Genetic Study of Interspecific Hybridization between the Red and Sika Deer in the Western Czech Republic

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1701
Author(s):  
Lenka Štohlová Putnová ◽  
Radek Štohl ◽  
Martin Ernst ◽  
Kateřina Svobodová
Keyword(s):  
Red Deer ◽  
Sika Deer ◽  
Molecular Genetic ◽  
Allelic Diversity ◽  
Molecular Genetic Analysis ◽  
Genetic Introgression ◽  
Statistical Framework ◽  
Western Bohemia ◽  
The Mean ◽  
Species Hybrids

Although inter-species hybrids between the red and sika deer can be phenotypically determined only exceptionally, there is the eventuality of identification via molecular genetic analysis. We used bi-parentally inherited microsatellite markers and a Bayesian statistical framework to re-examine the proportion of hybrids in the Czech red and sika deer populations. In total, 123 samples were collected, and the nuclear dataset consisted of 2668 allelic values. The number of alleles per locus ranged from 10 (BM1818) to 22 (BM888 and T193), yielding the mean of 16 alleles per locus across the deer. The mean allelic diversity of the red deer markedly exceeded that of the Japanese sika deer. Interspecific hybrids were detected, enabling us to confirm the genetic introgression of the sika deer into the red deer populations and vice versa in western Bohemia. The mean hybrid score equaled 10.6%, with 14.3% of the hybrids being among red deer–like individuals and 6.7% among sika-like ones. At two western Bohemian locations, namely, Doupovské hory and Slavkovský les, the total percentages of hybrid animals equaled 18.8 and 8.9, respectively. No red deer alleles were detected in the sika populations of the subregions of Kladská, Žlutice, and Lány. The NeighborNet network clearly separated the seven red and sika deer sampling populations according to the geography. The knowledge gained from the evaluated data is applicable in hunting management to reduce hybridization with the European deer.

scholarly journals Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere

2020 ◽  
Author(s):  
Fernando Lopes ◽  
Larissa R Oliveira ◽  
Amanda Kessler ◽  
Yago Beux ◽  
Enrique Crespo ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Molecular Data ◽  
Species Tree ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Data Types ◽  
High Coverage ◽  
Sea Lions ◽  
The Family

Abstract The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 to 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be non-monophyletic, with California (Z. californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Z. wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family.

Discriminating arboviral species

2021 ◽  
Vol 102 (4) ◽  
Author(s):  
Yiyuan Li ◽  
Angela C. O’Donnell ◽  
Howard Ochman
Keyword(s):  
Evolutionary History ◽  
Viral Vectors ◽  
Species Concept ◽  
International Committee ◽  
Biological Species ◽  
Biological Species Concept ◽  
Substantial Variation ◽  
Artificial Boundaries ◽  
Human Infections

Mosquito-borne arboviruses, including a diverse array of alphaviruses and flaviviruses, lead to hundreds of millions of human infections each year. Current methods for species-level classification of arboviruses adhere to guidelines prescribed by the International Committee on Taxonomy of Viruses (ICTV), and generally apply a polyphasic approach that might include information about viral vectors, hosts, geographical distribution, antigenicity, levels of DNA similarity, disease association and/or ecological characteristics. However, there is substantial variation in the criteria used to define viral species, which can lead to the establishment of artificial boundaries between species and inconsistencies when inferring their relatedness, variation and evolutionary history. In this study, we apply a single, uniform principle – that underlying the Biological Species Concept (BSC) – to define biological species of arboviruses based on recombination between genomes. Given that few recombination events have been documented in arboviruses, we investigate the incidence of recombination within and among major arboviral groups using an approach based on the ratio of homoplastic sites (recombinant alleles) to non-homoplastic sites (vertically transmitted alleles). This approach supports many ICTV-designations but also recognizes several cases in which a named species comprises multiple biological species. These findings demonstrate that this metric may be applied to all lifeforms, including viruses, and lead to more consistent and accurate delineation of viral species.

Not just a peep: The evolution of calling in Pseudacris crucifer

2018 ◽  
Author(s):  
Amanda Cicchino
Keyword(s):  
Reproductive Isolation ◽  
Full Range ◽  
Mate Recognition ◽  
Preliminary Evidence ◽  
Biological Species ◽  
Biological Species Concept ◽  
Incipient Species ◽  
Pseudacris Crucifer ◽  
Full Analysis ◽  
American Frog

Reproductive isolation is the hallmark of speciation as defined by the biological species concept. A species that is evolving towards reproductive isolation, but has not reached full isolation, is defined as an incipient species. One mechanism used by incipient species to further drive speciation is the use of mate recognition signals. The spring peeper, Pseudacris crucifer, is a North American frog that can be classified as an incipient species, as previous studies have found 6 distinct mitochondrial lineages within its range. Spring peepers use vocal signals for mate recognition and exhibit a female choice mating system where the males call to attract females. This study investigates the evolution of calling in spring peepers. Using calls from each lineage across the full range of spring peepers, I analyzed 11 different characteristics to determine whether the calls were different, and if so, which characteristics are being selected for. Preliminary evidence suggests that the calls between the lineages are distinct and that certain characteristics of the call are more heavily selected for than others. Full analysis on the data has not been completed at this time. This study will expand the understanding of the evolution of spring peepers, as well as offer insight into the role of mating systems on reproductive isolation.

Symbols and Dynamics of Social Meanings: Lessons From Residential Grave Spaces Among the Ekiti Yoruba of Southwest Nigeria

2019 ◽  
pp. 003022281986157 ◽  
Author(s):  
Babatunde Joshua Omotosho
Keyword(s):  
Social Structure ◽  
Symbolic Interactionism ◽  
Modern Society ◽  
Social Needs ◽  
Community Members ◽  
Policy Makers ◽  
Social Meanings ◽  
Southwest Nigeria ◽  
Modern Era ◽  
Power Play

Grave spaces within Yoruba (Nigeria) societies are not just ordinary symbols, and they constitute “other place” used to meet individuals’ physical and social needs. This study examined how residential grave spaces within Yoruba social structure are used by them in meeting their day-to-day needs. Drawing from symbolic interactionism theory, and data gathered from Ekiti-Yoruba culture, this study investigates how community members define and utilize the place of graves from traditional to modern society in meeting their needs. Findings revealed that during the precolonial society, grave spaces served religious and endearment purposes. While still retaining these functions in modern era, the functions have increased to security, protections, and power play due to the hurdles posed by modernity. The article concluded that the practice may continue in spite of its opposition by policy makers and orthodox faiths.

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