scholarly journals Genes and the species concept - How much of the genomes can be exchanged?

2019 ◽  
Author(s):  
Xinfeng Wang ◽  
Zixiao Guo ◽  
Shaohua Xu ◽  
Ming Yang ◽  
Qipian Chen ◽  
...  
Keyword(s):  
Species Concept ◽  
Biological Species ◽  
Biological Species Concept ◽  
Full Potential ◽  
Mangrove Species ◽  
Fine Grained ◽  
The Core ◽  
Mean Size ◽  
Species Specific ◽  
The Western Pacific

AbstractIn the biological species concept, much of the genomes cannot be exchanged between species1,2. In the modern genic view, species are distinct as long as genes that delineate the morphological, ecological and reproductive differences remain distinct2. The rest (or the bulk) of the genomes should be freely interchangeable. The core of the species concept therefore demands finding out thefull potentialof introgressions between species. In a survey of two closely related mangrove species (Rhizophora mucronataandR. stylosa) on the coasts of the western Pacific and Indian oceans, we found that the genomes are well delineated in allopatry, echoing their morphological and ecological divergence. The two species are sympatric/parapatric in the Daintree River area of northeastern Australia. In sympatry, their genomes harbor 7,700 and 3,100 introgression blocks, respectively, with each block averaging about 3-4 Kb. These fine-grained and strongly-penetrant introgressions suggest that each species must have evolved many differentially-adaptive (and, hence, non-introgressable) genes that contribute to speciation. We identify 30 such genes, seven of which are about flower development, within small genomic islets with a mean size of 1.4 Kb. In sympatry, the species-specific genomic islets account for only a small fraction (< 15%) of the genomes while the rest appears interchangeable.

scholarly journals Toward understanding the genetic mechanisms of speciation: Fine-grained introgressions between species

2020 ◽  
Author(s):  
Xinfeng Wang ◽  
Zixiao Guo ◽  
Shaohua Xu ◽  
Shao Shao ◽  
Sen Li ◽  
...  
Keyword(s):  
Gene Flow ◽  
De Novo ◽  
Biological Species ◽  
Adaptive Divergence ◽  
Biological Species Concept ◽  
Extensive Literature ◽  
Mangrove Species ◽  
Fine Grained ◽  
Genetic Mechanisms ◽  
Definition Of

Abstract The biological species concept (BSC) is the prevailing definition of species whereby genes cannot be exchanged during or after speciation. In contrast, since only genes that contribute to the adaptive divergence between species should be non-exchangeable, BSC appears to bear little relationship to the genetic process of speciation. The rejection of BSC demands evidence of continual gene flow until the completion of speciation. Here, we carry out the sequencing and de novo high-quality assembly of the genomes of two closely related mangrove species (Rhizophora mucronata and R. stylosa). Whole-genome re-sequencing of individuals from their distributions on the tropical coasts shows their genomes to be well delineated in allopatry. They became sympatric in northeastern Australia where their genomes harbor 9,963 and 3,874 introgression blocks, respectively, with each block averaging only about 3-4 Kb. These fine-grained introgressions indicate that gene flow continues even after numerous loci have evolved to become non-introgressable “genomic islets”. Many of these islets, only 1.4 Kb on average, harbor “speciation loci” which contribute to the divergence in flower development or gamete production and thus result in fitness reduction upon introgression. Our fine-grained analysis may thus be the first one to show that gene flow not only happens during speciation, but often continues until the completion of speciation. Under the weight of the extensive literature, BSC may deserve to be retired.

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.

scholarly journals Putting the Biological Species Concept to the Test: Using Mating Networks to Delimit Species

PLoS ONE ◽  
2013 ◽  
Vol 8 (6) ◽  
pp. e68267 ◽  
Author(s):  
Lélia Lagache ◽  
Jean-Benoist Leger ◽  
Jean-Jacques Daudin ◽  
Rémy J. Petit ◽  
Corinne Vacher
Keyword(s):  
Species Concept ◽  
Biological Species ◽  
Biological Species Concept

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.

The increasing multiplicity of the species concepts

2005 ◽  
Vol 176 (2) ◽  
pp. 221-225
Author(s):  
Jean Génermont
Keyword(s):  
Species Concept ◽  
Cladistic Analysis ◽  
Biological Species ◽  
Point Of View ◽  
Biological Species Concept ◽  
Phylogenetic Species ◽  
Phylogenetic Species Concept ◽  
Ecological Criteria ◽  
Stem Species ◽  
Definition Of

Abstract In 1980, Henri Tintant advocated the usefulness of the biological species concept in paleontology. At this time, this concept was still accepted by many neontologists, but it was already rather severely criticized by some others. In fact, a lot of new concepts appeared in the course of the following two decades. While a few ones are mere adjustments of the biological concept, for instance taking in account ecological criteria, in such a way that it could be applied to clonal organisms, some others, which were developed in connexion with the cladistic theory of taxonomy, are truly new from a conceptual point of view. The diagnosable version of the phylogenetic species concept is somewhat reminiscent of Simpson’s evolutionary species concept, since it accepts phyletic speciation as well as survival of the stem species after a cladogenetic event. One of its more criticizable features, from a cladistic point of view, is that the species are not necessarilly monophyletic. On another hand, according to the monophyly version of the phylogenetic species concept, species are recognized rather subjectively as monophyletic taxa revealed by some previous cladistic analysis dealing with operational taxonomic units. A consensus on the definition of species cannot be expected, since all concepts related to the biological one are founded on population grouping on the basis of potentially identical evolutionary fates, while those which are related to cladistic taxonomy are exclusively concerned with historical features.

scholarly journals Group selection and the development of the biological species concept

2010 ◽  
Vol 365 (1547) ◽  
pp. 1853-1863 ◽  
Author(s):  
James Mallet
Keyword(s):  
Species Concept ◽  
Biological Species ◽  
Second World War ◽  
Species Level ◽  
Biological Species Concept ◽  
Ernst Mayr ◽  
World War ◽  
Mutualistic Interaction ◽  
Theodosius Dobzhansky ◽  
Second World

The development of what became known as the biological species concept began with a paper by Theodosius Dobzhansky in 1935, and was amplified by a mutualistic interaction between Dobzhansky, Alfred Emerson and Ernst Mayr after the second world war. By the 1950s and early 1960s, these authors had developed an influential concept of species as coadapted genetic complexes at equilibrium. At this time many features of species were seen as group advantages maintained by selection to avoid breakdown of beneficial coadaptation and the ‘gene pool’. Speciation thus seemed difficult. It seemed to require, more so than today, an external deus ex machina , such as allopatry or the founder effect, rather than ordinary within-species processes of natural selection, sexual selection, drift and gene flow. In the mid-1960s, the distinctions between group and individual selection were clarified. Dobzhansky and Mayr both understood the implications, but their views on species changed little. These group selectionist ideas now seem peculiar, and are becoming distinctly less popular today. Few vestiges of group selectionism and species-level adaptationism remain in recent reviews of speciation. One wonders how many of our own cherished views on evolution will seem as odd to future biologists.

scholarly journals Collembola, the biological species concept and the underestimation of global species richness

2013 ◽  
Vol 22 (21) ◽  
pp. 5382-5396 ◽  
Author(s):  
Francesco Cicconardi ◽  
Pietro P. Fanciulli ◽  
Brent C. Emerson
Keyword(s):  
Species Richness ◽  
Species Concept ◽  
Biological Species ◽  
Biological Species Concept

scholarly journals Predictors of Taxonomic Inflation and its Role in Primate Conservation

2021 ◽  
Author(s):  
Maria J.A. Creighton ◽  
Alice Q. Luo ◽  
Simon M. Reader ◽  
Arne Ø. Mooers
Keyword(s):  
Perceived Risk ◽  
Species Concept ◽  
Research Effort ◽  
Biological Species ◽  
Primate Species ◽  
Biological Species Concept ◽  
Primate Conservation ◽  
Phylogenetic Species Concept ◽  
Initial Application ◽  
Positive Message

ABSTRACTSpecies are the main unit used to measure biodiversity, but different preferred diagnostic criteria can lead to very different delineations. For instance, named primate species have more than doubled since 1982. Such increases have been termed “taxonomic inflation” and have been attributed to the widespread adoption of the ‘phylogenetic species concept’ (PSC) in preference to the previously popular ‘biological species concept’ (BSC). Criticisms of the PSC have suggested taxonomic inflation may be biased toward particular taxa and have unfavourable consequences for conservation. Here, we explore predictors of taxonomic inflation across primate taxa since the initial application of the PSC nearly 40 years ago. We do not find evidence that diversification rate, the rate of lineage formation over evolutionary time, is linked to inflation, contrary to expectations if the PSC identifies incipient species. We also do not find evidence of research effort in fields where work has been suggested to motivate splitting being associated with increases in species numbers among genera. To test the suggestion that splitting groups is likely to increase their perceived risk of extinction, we test whether genera that have undergone more splitting have also observed a greater increase in their proportion of threatened species since the introduction of the PSC. We find no cohesive signal of inflation leading to higher threat probabilities across primate genera. Overall, this analysis sends a positive message that threat statuses of primate species are not being overwhelmingly affected by splitting in line with what has recently been reported for birds. Regardless, we echo warnings that it is unwise for conservation to be reliant on taxonomic stability. Species (however defined) are not independent from one another, thus, monitoring and managing them as such may not meet the overarching goal of conserving biodiversity.

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.

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