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.

scholarly journals Genetic diversity and structure of the binturong Arctictis binturong (Carnivora: Viverridae) – status of the elusive Palawan binturong and implications for conservation

2019 ◽  
Author(s):  
Géraldine Veron ◽  
Agathe Debruille ◽  
Pauline Kayser ◽  
Desamarie Antonette P Fernandez ◽  
Aude Bourgeois
Keyword(s):  
Taxonomic Status ◽  
The Philippines ◽  
The Other ◽  
Restricted Range ◽  
Crucial Importance ◽  
Separate Species ◽  
Mitochondrial Markers ◽  
Molecular Approaches ◽  
Captive Populations ◽  
Genetic Diversity And Structure

Abstract The binturong or bearcat is a forest mesocarnivore ranging from Nepal to Indonesia and the Philippines. Several subspecies of binturongs are recognized but a revision is needed. The binturong from Palawan was described as a species and is now considered a subspecies, but its status has never been checked using molecular approaches. Owing to its restricted range and the pressure on its habitat, the Palawan binturong may be endangered. It is, therefore, of crucial importance to clarify its taxonomic status, particularly for the management of captive populations. We sequenced one nuclear and two mitochondrial markers for binturongs from locations across the species range and from zoos. Our results provide an assessment of the genetic polymorphism and structure within the binturong, resulting in two groups, corresponding to the Indochinese and the Sundaic regions. Within the latter were found the Palawan binturongs on one side, and an individual from Sulu archipelago (a locality not reported before) on the other side. The Palawan binturongs form a monophyletic group, genetically close to Bornean binturongs, which suggests that they may have dispersed from Borneo, and represents a lineage worth preserving, but which is not a separate species nor a separate subspecies.

scholarly journals Variation and Diagnostic Power of the Internal Transcribed Spacer 2 in Mediterranean and Atlantic Eolid Nudibranchs (Mollusca, Gastropoda)

2021 ◽  
Vol 8 ◽  
Author(s):  
Matteo Garzia ◽  
Paolo Mariottini ◽  
Daniele Salvi ◽  
Giulia Furfaro
Keyword(s):  
Species Delimitation ◽  
Internal Transcribed Spacer ◽  
Morphological Characters ◽  
Marine Biodiversity ◽  
Cryptic Diversity ◽  
Nuclear Marker ◽  
Nuclear Markers ◽  
Closely Related Species ◽  
Internal Transcribed Spacer 2 ◽  
Mitochondrial Markers

Mediterranean marine biodiversity is still underestimated especially for groups such as nudibranchs. The identification of nudibranchs taxa is challenging because few morphological characters are available and among them chromatic patterns often do not align with species delimitation. Molecular assessments helped unveiling cryptic diversity within nudibranchs and have been mostly based on mitochondrial markers. Fast evolving nuclear markers are much needed to complement phylogenetic and systematic assessments at the species and genus levels. Here, we assess the utility of the nuclear Internal Transcribed Spacer 2 (ITS2) to delimit species in the eolid nudibranchs using both primary and secondary structures. Comparisons between the variation observed at the ITS2 and at the two commonly used mitochondrial markers (COI and 16S) on 14 eolid taxa from 10 genera demonstrate the ability of ITS2 to detect congeneric, closely related, species. While ITS2 has been fruitfully used in several other mollusc taxa, this study represents the first application of this nuclear marker in nudibranchs.

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 DIFFERENCES IN ADRENAL MORPHOLOGY IN MALE DARK AGOUTI, SPRAGUE-DAWLEY AND WISTAR RATS

1999 ◽  
Vol 47 (3) ◽  
pp. 335-339 ◽  
Author(s):  
Jenny M. Wilkinson ◽  
S. Halley ◽  
P. A. Towers
Keyword(s):  
Wistar Rats ◽  
Adrenal Glands ◽  
Volume Fraction ◽  
Single Species ◽  
The Other ◽  
Dark Agouti ◽  
Sprague Dawley ◽  
Zona Reticularis ◽  
Functional Differences ◽  
Morphological Differences

There is little published information describing the differences in adrenal structure between strains of a single species despite quite well known functional differences. In this paper we report morphological differences in the adrenal glands between three strains of laboratory rat; Dark Agouti (DA), Sprague-Dawley (SD) and Wistar (W). Significant differences in adrenal weights (as a percentage of body weight) were not detected between any of the groups. While there were no significant differences in the volume of medullary or zonae glomerulosa or fasciculata tissue, the volume fraction for the zona reticularis was significantly smaller in DAs compared to the other strains. The functional significance of these differences is unknown. However, it is suggested that the reduced volume of zona reticularis tissue may contribute to a reduced capacity for glucocorticoid synthesis or storage.

scholarly journals A taxonomic revision of Phytophthora Clade 5 including two new species, Phytophthora agathidicida and P. cocois

Phytotaxa ◽  
2015 ◽  
Vol 205 (1) ◽  
pp. 21 ◽  
Author(s):  
Bevan Simon Weir ◽  
ELSA P. PADERES ◽  
NITISH ANAND ◽  
JANICE Y. UCHIDA ◽  
SHAUN R. PENNYCOOK ◽  
...  
Keyword(s):  
New Species ◽  
Pacific Islands ◽  
Cocos Nucifera ◽  
Taxonomic Revision ◽  
The Other ◽  
Separate Species ◽  
The Pacific ◽  
Two New Species ◽  
Morphological Differences ◽  
Species Descriptions

Phytophthora Clade 5 is a very poorly studied group of species of oomycete chromists, consisting of only two known species P. castaneae (≡ P. katsurae, nom. illegit.) and P. heveae with most isolates from East Asia and the Pacific Islands. However, isolates of two important disease-causing chromists in Clade 5, one of kauri (Agathis australis) in New Zealand, the other of coconut (Cocos nucifera) in Hawaii, poorly match the current species descriptions. To verify whether these isolates belong to separate species a detailed morphological study and phylogenetic analysis consisting of eight genetic loci was conducted. On the basis of genetic and morphological differences and host specificity, we present the formal description of two new species in Clade 5, Phytophthora agathidicida sp. nov. and Phytophthora cocois sp. nov. To clarify the typification of the other Clade 5 species, an authentic ex-holotype culture of Phytophthora castaneae is designated and P. heveae is lectotypified and epitypified.

scholarly journals Species delimitation of Margattea cockroaches from China, with seven new species (Blattodea, Ectobiidae, Pseudophyllodromiinae)

ZooKeys ◽  
2021 ◽  
Vol 1036 ◽  
pp. 121-151
Author(s):  
Jia-Jun He ◽  
Du-Ting Jin ◽  
Yi-Shu Wang ◽  
Yan-Li Che ◽  
Zong-Qing Wang
Keyword(s):  
New Species ◽  
Confidence Interval ◽  
Genetic Distance ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Operational Taxonomic Units ◽  
As Species ◽  
The Difference ◽  
Morphological Differences ◽  
Barcode Gap

Nearly 450 Margattea specimens were collected from 27 locations in China and their morphology was examined. Then 68 Margattea COI sequences were obtained and used to carry out phylogenetic analyses as well as species delimitation analyses using General Mixed Yule Coalescent (GMYC), Automatic Barcode Gap Discovery (ABGD), and Poisson Tree Processes (bPTP). GMYC analysis resulted in 21 molecular operational taxonomic units (MOTUs) (confidence interval: 20–22), which was completely consistent with the result of the bPTP. There were 15 MOTUs using the ABGD method. The number of MOTUs was slightly different from the assigned morphospecies (16). As to the incongruence between molecular and morphological results, we checked the specimens again and made sure that most morphological differences were determined to be intraspecific differences (except the difference between M. angusta and M. mckittrickae), although a large genetic distance existed. Finally, 16 Margattea species from China were defined in this study, of which, seven new species are established, i.e. Margattea deltodonta J-J He & Z-Q Wang, sp. nov., Margattea cuspidata J-J He & Z-Q Wang, sp. nov., Margattea caudata J-J He & Z-Q Wang, sp. nov., Margattea paratransversa J-J He & Z-Q Wang, sp. nov., Margattea disparilis J-J He & Z-Q Wang, sp. nov., Margattea transversa J-J He & Z-Q Wang, sp. nov., and Margattea bicruris J-J He & Z-Q Wang, sp. nov.

Bipartite molecular approach for species delimitation and resolving cryptic speciation of Exobasidium vexans within the Exobasidium genus

2021 ◽  
Vol 92 ◽  
pp. 107496
Author(s):  
Chayanika Chaliha ◽  
V. Chandra Kaladhar ◽  
Robin Doley ◽  
Praveen Kumar Verma ◽  
Aditya Kumar ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Cryptic Speciation ◽  
Molecular Approach

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.

scholarly journals Two Cases of Gelsemium Elegans Benth. Poisoning

2007 ◽  
Vol 14 (4) ◽  
pp. 221-224 ◽  
Author(s):  
HT Fung ◽  
KK Lam ◽  
SK Lam ◽  
OF Wong ◽  
CW Kam
Keyword(s):  
Respiratory Failure ◽  
General Public ◽  
The Other ◽  
Respiratory Support ◽  
Close Monitoring ◽  
Morphological Differences

A couple of spouse mistook the Gelsemium elegans Benth. collected in countryside for Mussaenda pubescens Ait. f. and suffered toxicity soon after ingestion. One went into respiratory failure necessitating intubation and the other developed dizziness. The morphological differences between Gelsemium elegans Benth. and Mussaenda pubescens Ait. f. may not be easily recognised by the general public. Close monitoring and respiratory support are the cornerstones of management.

scholarly journals Rape and the Prevalence of Hybrids in Broadly Sympatric Species: a Case Study using Albatrosses

2014 ◽  
Author(s):  
Sievert Rohwer ◽  
Rebecca B. Harris ◽  
Hollie E. Walsh
Keyword(s):  
Species Differences ◽  
Field Studies ◽  
Sympatric Species ◽  
Male Reproductive Success ◽  
Gene Exchange ◽  
Nuclear Markers ◽  
Mitochondrial Markers ◽  
Extensive Field

Conspecific rape often increases male reproductive success. However, the haste and aggression of forced copulations suggests that males may sometimes rape heterospecific females, thus making rape a likely, but undocumented, source of hybrids between broadly sympatric species. We present evidence that heterospecific rape may be the source of hybrids between Black-footed and Laysan Albatrosses (Phoebastria nigripes, and P. immutabilis, respectively). Extensive field studies have shown that paired (but not unpaired) males of both of these albatross species use rape as a supplemental reproductive strategy. Between species differences in size, timing of laying, and aggressiveness suggest that Black-footed Albatrosses should be more successful than Laysan Albatrosses in heteropspecific rape attempts, and male Black-footed Albatrosses have been observed attempting to force copulations on female Laysan Albatrosses. Nuclear markers showed that the six hybrids we studied were F1s and mitochondrial markers showed that male Black-footed Albatrosses sired all six hybrids. The siring asymmetry found in our hybrids may have long persisted because an IM analysis suggests that long-term gene exchange between these species has been from Black-footed Albatrosses into Laysan Albatrosses. If hybrids are sired in heterospecific rapes, they presumably would be raised and sexually imprinted on Laysan Albatrosses, and two unmated hybrids in a previous study courted only Laysan Albatrosses.

Sign in / Sign up

Export Citation Format

Share Document