scholarly journals Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation

2019 ◽  
Vol 286 (1900) ◽  
pp. 20182924 ◽  
Author(s):  
Carmen del R. Pedraza-Marrón ◽  
Raimundo Silva ◽  
Jonathan Deeds ◽  
Steven M. Van Belleghem ◽  
Alicia Mastretta-Yanes ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Population Genomics ◽  
Single Species ◽  
Red Snapper ◽  
Nominal Species ◽  
Lutjanus Campechanus ◽  
Separate Species ◽  
Western Atlantic ◽  
Species Population ◽  
Genome Wide Data

Species delimitation is a major quest in biology and is essential for adequate management of the organismal diversity. A challenging example comprises the fish species of red snappers in the Western Atlantic. Red snappers have been traditionally recognized as two separate species based on morphology: Lutjanus campechanus (northern red snapper) and L. purpureus (southern red snapper). Recent genetic studies using mitochondrial markers, however, failed to delineate these nominal species, leading to the current lumping of the northern and southern populations into a single species ( L. campechanus ). This decision carries broad implications for conservation and management as red snappers have been commercially over-exploited across the Western Atlantic and are currently listed as vulnerable. To address this conflict, we examine genome-wide data collected throughout the range of the two species. Population genomics, phylogenetic and coalescent analyses favour the existence of two independent evolutionary lineages, a result that confirms the morphology-based delimitation scenario in agreement with conventional taxonomy. Despite finding evidence of introgression in geographically neighbouring populations in northern South America, our genomic analyses strongly support isolation and differentiation of these species, suggesting that the northern and southern red snappers should be treated as distinct taxonomic entities.

scholarly journals The genomic revolution and species delimitation in birds (and other organisms): gene flow matters, but what about other evolutionary forces?

2020 ◽  
Author(s):  
Carlos Daniel Cadena ◽  
Felipe Zapata
Keyword(s):  
Gene Flow ◽  
Phenotypic Variation ◽  
Species Delimitation ◽  
Population Level ◽  
Species Limits ◽  
Evolutionary Forces ◽  
Species Population ◽  
Genome Wide Data ◽  
Evolutionary Lineages

Given the notion that species are population-level lineages and the availability of genomic data to identify separately evolving populations, researchers usually establish species limits based on gene flow or lack thereof. A strict focus on gene flow as the main –or only– criterion to delimit species involves two main complications in practice. First, approaches often used to apply this criterion to genome-wide data cannot by themselves distinguish species limits from within-species population structure, particularly in allopatric organisms. Second, recognizing as species only those lineages one can identify using such approaches fails to embrace the role of other evolutionary forces (i.e. various forms of selection) in defining evolutionary lineages. Using examples from various groups of birds, we call for the importance of considering evolutionary forces additional to gene flow in species delimitation and explain why genomic approaches commonly used in taxonomic studies may be insufficient by themselves to properly uncover species limits. By considering the processes that structure genotypic and phenotypic variation during speciation, we argue that rigorous analyses of phenotypic variation remain crucial for species delimitation in the genomics era because phenotypes uniquely inform us about the role of selection maintaining the cohesion of evolutionary lineages. Evolutionary theory describing the roles of gene flow, genetic drift and natural selection in the origin and maintenance of species calls for an integration of genomics with phenomics in avian species delimitation.

scholarly journals Testing species hypotheses for Fridericia magna, an enchytraeid worm (Annelida: Clitellata) with great mitochondrial variation

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Svante Martinsson ◽  
Mårten Klinth ◽  
Christer Erséus
Keyword(s):  
Species Delimitation ◽  
Single Species ◽  
The Other ◽  
Cryptic Speciation ◽  
Incipient Speciation ◽  
Nuclear Markers ◽  
Separate Species ◽  
Mitochondrial Markers ◽  
Morphological Differences ◽  
Barcode Gap

Abstract Background Deep mitochondrial divergences were observed in Scandinavian populations of the terrestrial to semi-aquatic annelid Fridericia magna (Clitellata: Enchytraeidae). This raised the need for testing whether the taxon is a single species or a complex of cryptic species. Results A total of 62 specimens from 38 localities were included in the study, 44 of which were used for species delimitation. First, the 44 specimens were divided into clusters using ABGD (Automatic Barcode Gap Discovery) on two datasets, consisting of sequences of the mitochondrial markers COI and 16S. For each dataset, the worms were divided into six not completely congruent clusters. When they were combined, a maximum of seven clusters, or species hypotheses, were obtained, and the seven clusters were used as input in downstream analyses. We tested these hypotheses by constructing haplowebs for two nuclear markers, H3 and ITS, and in both haplowebs the specimens appeared as a single species. Multi-locus species delimitation analyses performed with the Bayesian BPP program also mainly supported a single species. Furthermore, no apparent morphological differences were found between the clusters. Two of the clusters were partially separated from each other and the other clusters, but not strongly enough to consider them as separate species. All 62 specimens were used to visualise the Scandinavian distribution, of the species, and to compare with published COI data from other Fridericia species. Conclusion We show that the morphospecies Fridericia magna is a single species, harbouring several distinct mitochondrial clusters. There is partial genetic separation between some of them, which may be interpreted as incipient speciation. The study shows the importance of rigorous species delimitation using several independent markers when deep mitochondrial divergences might give the false impression of cryptic speciation.

New synonymies among species of Brontostoma (Hemiptera: Heteroptera: Reduviidae)

Zootaxa ◽  
2020 ◽  
Vol 4869 (3) ◽  
pp. 301-325
Author(s):  
HÉLCIO R. GIL-SANTANA
Keyword(s):  
Intraspecific Variation ◽  
Male Genitalia ◽  
French Guiana ◽  
General Structure ◽  
Single Species ◽  
Nominal Species ◽  
Separate Species ◽  
Neotropical Species ◽  
First Time

The presence of the same general structure and vestiture, an overall similarity in coloration with merely a few minor differences, a broad range of intraspecific variation with several intermediate color varieties forms, and the similar structure of the male genitalia in three Neotropical species of Brontostoma Kirkaldy, 1904 (Hemiptera: Heteroptera: Reduviidae: Ectrichodiinae) led to the hypothesis that all of them represent a single species, resulting in the following newly proposed subjective synonymies: B. basalis (Stål, 1859) = B. sanguinosum (Stål, 1872), syn. nov. = B. pallitarsis (Walker, 1873), syn. nov. The male genitalia of another nominal species, B. infensum Wygodzinsky, 1951, showed a set of differences which are judged to sufficiently support the recognition of it as a separate species. Intraspecific morphological and color variations of B. basalis are documented and discussed, and this species is recorded from French Guiana for the first time. 

scholarly journals Population Structure of Lutjanus purpureus (Lutjanidae - Perciformes) on the Brazilian coast: further existence evidence of a single species of red snapper in the western Atlantic

2012 ◽  
Vol 84 (4) ◽  
pp. 979-999 ◽  
Author(s):  
Grazielle Gomes ◽  
Iracilda Sampaio ◽  
Horacio Schneider
Keyword(s):  
Population Structure ◽  
Control Region ◽  
Single Species ◽  
Mitochondrial Control Region ◽  
Haplotype Network ◽  
Molecular Data ◽  
Red Snapper ◽  
Brazilian Coast ◽  
Base Pairs ◽  
Western Atlantic

The present study focus on the mitochondrial control region to investigate phylogeographic patterns and population structure in Lutjanus purpureus, and to evaluate the genetic similarity between L. purpureus and L. campechanus. For the initial analysis, 810 base pairs sequence from control region were obtained from 239 specimens of L. purpureus collected from four localities off the Brazilian coast. The results revealed the presence of a single panmictic population characterized by high values of genetic diversity. The 299 base pairs hypervariable portion were used for the combined analysis of L. purpureus and L. campechanus, being 275 haplotypes identified in the 414 specimens. Phylogenetic tree and haplotype network did not indicate phylogeographic substructuring between the two species, but rather an intense intermingling of individuals. Considering their marked morphological similarity, the molecular data presented here indicate that only one species of red snapper exists in the western Atlantic.

scholarly journals Survival analysis of a stochastic delay single-species system in polluted environment with psychological effect and pulse toxicant input

2020 ◽  
Vol 2020 (1) ◽  
Author(s):  
Xiangjun Dai ◽  
Suli Wang ◽  
Weizhi Xiong ◽  
Ni Li
Keyword(s):  
Sufficient Conditions ◽  
Single Species ◽  
Threshold Value ◽  
Psychological Effect ◽  
Polluted Environment ◽  
Population System ◽  
Stochastic Delay ◽  
Species Population ◽  
The Mean ◽  
Single Species Population

Abstract We propose and study a stochastic delay single-species population system in polluted environment with psychological effect and pulse toxicant input. We establish sufficient conditions for the extinction, nonpersistence in the mean, weak persistence, and strong persistence of the single-species population and obtain the threshold value between extinction and weak persistence. Finally, we confirm the efficiency of the main results by numerical simulations.

Spawning of Red Snapper (Lutjanus campechanus) in Response to Hormonal Induction or Environmental Control in a Hatchery Setting

2009 ◽  
Vol 17 (2) ◽  
pp. 149-155 ◽  
Author(s):  
R. P. Phelps ◽  
N. Papanikos ◽  
B. D. Bourque ◽  
F. T. Bueno ◽  
R. P. Hastey ◽  
...  
Keyword(s):  
Environmental Control ◽  
Red Snapper ◽  
Lutjanus Campechanus ◽  
Hormonal Induction

Patterns of morphological diversity among and within arcid bivalve species pairs separated by the Isthmus of Panama

2001 ◽  
Vol 75 (3) ◽  
pp. 590-606 ◽  
Author(s):  
Peter B. Marko ◽  
Jeremy B. C. Jackson
Keyword(s):  
Morphological Variation ◽  
Fossil Record ◽  
Eastern Pacific ◽  
Nominal Species ◽  
Western Atlantic ◽  
Isthmus Of Panama ◽  
Species Pairs ◽  
Recent Species ◽  
Discriminant Analyses ◽  
Collection Sites

Geminate species are morphologically similar sister-species found on either side of the Isthmus of Panama. The existence of all geminates in the tropical Eastern Pacific ocean and the Caribbean Sea is most often explained by vicariance: closure of the Central American Seaway 3.1 to 3.5 Ma simultaneously isolated populations of species with amphi-American distributions. In this paper, we test the potential of morphological measurements for discriminating between Recent geminate species pairs from three genera (Arca, Arcopsis, and Barbatia) in the bivalve family Arcidae and examine the prospects for distinguishing nominal species in the fossil record. Fourteen morphological variables were used to characterize shell shape and multivariate methods were used to discriminate between five Recent species pairs. Collection sites were also used as a priori groups for discrimination to describe patterns of intraspecific morphological variation and to evaluate differences among samples from different geographic regions.On average, 84 percent of specimens within geminate pairs are classified correctly following five separate discriminant analyses with nominal species as the grouping variable. Although all but one arcid species pair are discriminated with high statistical significance, some collection sites within species are highly morphologically distinct. Overall, a large proportion of specimens from each collection locality (79 percent on average) can be classified correctly to site although no single site possessed a multivariate centroid that was significantly different from all other conspecific centroids. The distinctiveness of some collection sites, however, raises the possibility that some nominal species may harbor cryptic species, indicating the need for wider geographic surveys of both molecular and morphological variation within geminate species pairs.The eigenvalue coefficients derived from the Recent samples of one geminate pair (Arca mutabilis and A. imbricata) were used to assess the potential for identifying arcid species in the fossil record. Discriminant analyses of fossil Arca indicate that the forms that characterize Recent A. mutabilis and A. imbricata are present in the fossil record as far back as the Late Early Miocene, in the Cantaure Formation of Venezuela. Because a deep water connection between the Eastern Pacific and Western Atlantic existed until the Middle Miocene, the morphological differences associated with Recent A. mutabilis and A. imbricata likely existed well before the rising Isthmus affected ocean circulation patterns in tropical America. Therefore, despite great overall morphological similarity, these putative geminate species likely have a time of divergence that is at least four times older than final seaway closure. The geographic distribution of fossils also suggests that morphological forms associated with each Recent species had amphi-American distributions both before and after isthmus formation but are now geographically restricted to either side of the isthmus in the Recent fauna.

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

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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