Echinoderms are marine water invertebrates that are represented by more than 7000 extant species, grouped in five classes and showing diverse morphologies (starfish, sea lilies, feather stars, sea ...urchins, sea cucumbers, brittle and basket stars). In an effort to further study their diversity, DNA barcodes (DNA fragments of the 5’ end of the cytochrome c oxidase subunit I gene, COI) have been used to complement morphological examination in identifying evolutionary lineages. Although divergent clusters of COI sequences were reported to generally match morphological species delineations, they also revealed some discrepancies, suggesting overlooked species, ecophenotypic variation or multiple COI lineages within one species. Here, we sequenced COI fragments of 312 shallow-water echinoderms of the East Coast of South Africa (KwaZulu-Natal Province) and compared morphological identifications with species delimitations obtained with four methods that are exclusively based on COI sequences. We identified a total of 103 morphospecies including 18 that did not exactly match described species. We also report 46 COI sequences that showed large divergences (>5% p-distances) with those available to date and publish the first COI sequences for 30 species. Our analyses also identified discordances between morphological identifications and COI-based species delimitations for a considerable proportion of the morphospecies studied here (49/103). For most of them, further investigation is necessary to keep a sound connection between taxonomy and the growing importance of DNA-based research.
DNA barcoding of non-avian reptiles based on the cytochrome oxidase subunit I (COI) gene is still in a very early stage, mainly due to technical problems. Using a newly developed set of ...reptile-specific primers for COI we present the first comprehensive study targeting the entire reptile fauna of the fourth-largest island in the world, the biodiversity hotspot of Madagascar.
Representatives of the majority of Madagascan non-avian reptile species (including Squamata and Testudines) were sampled and successfully DNA barcoded. The new primer pair achieved a constantly high success rate (72.7-100%) for most squamates. More than 250 species of reptiles (out of the 393 described ones; representing around 64% of the known diversity of species) were barcoded. The average interspecific genetic distance within families ranged from a low of 13.4% in the Boidae to a high of 29.8% in the Gekkonidae. Using the average genetic divergence between sister species as a threshold, 41-48 new candidate (undescribed) species were identified. Simulations were used to evaluate the performance of DNA barcoding as a function of completeness of taxon sampling and fragment length. Compared with available multi-gene phylogenies, DNA barcoding correctly assigned most samples to species, genus and family with high confidence and the analysis of fewer taxa resulted in an increased number of well supported lineages. Shorter marker-lengths generally decreased the number of well supported nodes, but even mini-barcodes of 100 bp correctly assigned many samples to genus and family.
The new protocols might help to promote DNA barcoding of reptiles and the established library of reference DNA barcodes will facilitate the molecular identification of Madagascan reptiles. Our results might be useful to easily recognize undescribed diversity (i.e. novel taxa), to resolve taxonomic problems, and to monitor the international pet trade without specialized expert knowledge.
Delimiting species in facultatively selfing taxa is a challenging problem of which the terrestrial pulmonate snail genus Rumina is a good example. These snails have a mixed breeding system and show a ...high degree of shell and color variation. Three nominal species (R. decollata, R. saharica and R. paivae) and two color morphs within R. decollata (dark and light) are currently recognized. The present study aims at evaluating to what extent these entities reflect evolutionary diverging taxonomic units, rather than fixed polymorphisms due to sustained selfing. Therefore, a phylogenetic analysis of nuclear (ITS1, ITS2) and mitochondrial DNA (COI, CytB, 12S rDNA, 16S rDNA) sequences was performed. Putative species in Rumina, inferred from the mitochondrial DNA phylogeny, were compared with those proposed on the basis of the COI gene by (1) DNA barcoding gap analysis, (2) Automatic Barcode Gap Discovery, (3) the species delimitation plug-in of the Geneious software, (4) the Genealogical Sorting Index, and (5) the General Mixed Yule Coalescent model. It is shown that these methods produce a variety of different species hypotheses and as such one may wonder to what extent species delimitation methods are really useful. With respect to Rumina, the data suggest at least seven species, one corresponding to R. saharica and six that are currently grouped under the name R. decollata. The species-level status of R. paivae is rejected.
Eurythenes gryllus is one of the most widespread amphipod species, occurring in every ocean with a depth range covering the bathyal, abyssal and hadal zones. Previous studies, however, indicated the ...existence of several genetically and morphologically divergent lineages, questioning the assumption of its cosmopolitan and eurybathic distribution. For the first time, its genetic diversity was explored at the global scale (Arctic, Atlantic, Pacific and Southern oceans) by analyzing nuclear (28S rDNA) and mitochondrial (COI, 16S rDNA) sequence data using various species delimitation methods in a phylogeographic context. Nine putative species-level clades were identified within E. gryllus. A clear distinction was observed between samples collected at bathyal versus abyssal depths, with a genetic break occurring around 3,000 m. Two bathyal and two abyssal lineages showed a widespread distribution, while five other abyssal lineages each seemed to be restricted to a single ocean basin. The observed higher diversity in the abyss compared to the bathyal zone stands in contrast to the depth-differentiation hypothesis. Our results indicate that, despite the more uniform environment of the abyss and its presumed lack of obvious isolating barriers, abyssal populations might be more likely to show population differentiation and undergo speciation events than previously assumed. Potential factors influencing species' origins and distributions, such as hydrostatic pressure, are discussed. In addition, morphological findings coincided with the molecular clades. Of all specimens available for examination, those of the bipolar bathyal clade seemed the most similar to the 'true' E. gryllus. We present the first molecular evidence for a bipolar distribution in a macro-benthic deep-sea organism.
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•RADseq successfully resolved taxonomic and phylogenetic problems in Pyramidula.•Phylogenetic relationships among species were fully resolved.•D-statistics provided no or weak ...evidence of ancestral interspecific hybridization.•The best species delimitation scenario distinguished nine species in Europe.
Restriction site-associated DNA sequencing (RADseq) was used to jointly assess phylogenetic relationships, interspecific hybridization and species delimitation in the cryptic, non-model land snail complex Pyramidula. A robust phylogeny was inferred using a matrix of concatenated sequences of almost 1,500,000bp long, containing >97,000 polymorphic sites. Maximum likelihood analyses fully resolved the phylogenetic relationships among species and drastically improved phylogenetic trees obtained from mtDNA and nDNA gene trees (COI, 16S rRNA, 5.8S rRNA, ITS2 and 28S rRNA sequence data). The best species delimitation scenario was selected on the basis of 875 unlinked single nucleotide polymorphisms, showing that nine Pyramidula species should be distinguished in Europe. Applying D-statistics provided no or weak evidence of interspecific hybridization among Pyramidula, except for some evidence of gene flow between two species.
Sea cucumber taxonomy and systematics has in the past heavily relied on gross external and internal anatomy, ossicle assemblage in different tissues, and molecular characterisation, with coloration, ...habitat, and geographical and bathymethric distribution also considered important parameters. In the present paper, we made these observations and techniques in detail and complemented them with the novel technique of micro-computed tomography of the calcareous ring. We investigated a single European species, the so-called gravel sea cucumber,
Neopentadactyla mixta
(Östergren, 1898), using recently collected material from the Chausey Islands, Normandy, France. We redescribed the species, illustrated its ossicle assemblage through scanning electron microscopy, and visualised the calcareous ring through stacking photography and through micro-CT scanning. Additionally, a DNA fragment of 955 base pairs of the 18S ribosomal RNA gene was sequenced from one specimen, which showed a high similarity with the only sequence of
N. mixta
publicly available. We completed this integrative study by providing a detailed distribution of the occurrence of
N. mixta
based on published, verifiable accounts.
Species and populations are disappearing at an alarming rate as a direct result of human activities. Loss of genetic diversity associated with population decline directly impacts species' long-term ...survival. Therefore, preserving genetic diversity is of considerable conservation importance. However, to assist in conservation efforts, it is important to understand how genetic diversity is spatially distributed and how it changes due to anthropogenic pressures. In this study, we use historical museum and modern faecal samples of two critically endangered eastern gorilla taxa, Grauer's (Gorilla beringei graueri) and mountain gorillas (Gorilla beringei beringei), to directly infer temporal changes in genetic diversity within the last century. Using over 100 complete mitochondrial genomes, we observe a significant decline in haplotype and nucleotide diversity in Grauer's gorillas. By including historical samples from now extinct populations we show that this decline can be attributed to the loss of peripheral populations rather than a decrease in genetic diversity within the core range of the species. By directly quantifying genetic changes in the recent past, our study shows that human activities have severely impacted eastern gorilla genetic diversity within only four to five generations. This rapid loss calls for dedicated conservation actions, which should include preservation of the remaining peripheral populations.
In many species, individuals can develop into strikingly different morphs, which are determined by a simple Mendelian locus. How selection shapes loci that control complex phenotypic differences ...remains poorly understood. In the spider Oedothorax gibbosus, males develop either into a 'hunched' morph with conspicuous head structures or as a fast-developing 'flat' morph with a female-like appearance. We show that the hunched-determining allele contains a unique genomic fragment of approximately 3 megabases that is absent in the flat-determining allele. This fragment comprises dozens of genes that duplicated from genes found at the same as well as different chromosomes. All functional duplicates, including a duplicate of the key sexual differentiation regulatory gene doublesex, show male-specific expression, which illustrates their integrated role as a masculinizing supergene. Our findings demonstrate how extensive indel polymorphisms and duplications of regulatory genes may contribute to the evolution of co-adapted gene clusters, sex-limited reproductive morphs and the enigmatic evolution of exaggerated sexual traits in general.
This study aimed to explore the species diversity within the isopod genus Metastenasellus in Benin and Cameroon. Compared to other parts of the world, the described diversity of stygobiotic ...crustaceans in Africa is low due to a dearth of studies and taxonomic expertise. However, recent research activities in Benin and Cameroon suggest higher groundwater diversity than previously envisioned. Recent sampling campaigns in these countries have shown that Metastenasellus is a major group in the underground aquatic environment. The accumulation of biological material provided an opportunity to explore species diversity within the genus using a DNA taxonomy approach based on the cytochrome c oxidase subunit I (COI) gene fragment.
While the leaf insects (Phylliidae) are a well-supported group within Phasmatodea, the genus
Illiger, 1798 has repeatedly been recovered as paraphyletic. Here, the Phyllium (Phyllium) celebicum ...species group is reviewed and its distinctiveness from the remaining Phylliini genera and subgenera in a phylogenetic context based on morphological review and a phylogenetic analysis of three genes (nuclear gene 28S and mitochondrial genes COI and 16S) from most known and multiple undescribed species is shown. A new genus,
, is erected to partially accommodate the former members of the
species group. Two species,
Hennemann et al., 2009 and
Lit & Eusebio, 2014 morphologically and molecularly do not fall within this clade and are therefore left within Phyllium (Phyllium). The transfer of the remaining
group members from
Illiger, 1798 to this new genus creates the following new combinations;
(Westwood, 1859),
;
(de Haan, 1842),
;
(Seow-Choen, 2017),
;
(Yang, 1995),
;
(Cumming & Le Tirant, 2020),
;
(Liu, 1993),
;
(Liu, 1993),
;
(Liu, 1993),
;
(Wood-Mason, 1875),
;
(Cumming & Teemsma, 2018),
; and
(Liu, 1993),
The review of specimens belonging to this clade also revealed 13 undescribed species, which are described within as:
from Vietnam: Quang Nam Province;
from Vietnam: Quang Ngai, Thua Thien Hue, Da Nang, Gia Lai, Quang Nam, and Dak Nong Provinces;
from Vietnam: Ninh Thuan Province;
from China: Yunnan Province;
from Indonesia: Wangi-wangi Island;
from Vietnam: Quang Ngai and Lam Dong Provinces;
from Vietnam: Lam Dong and Dak Lak Provinces;
from Cambodia: Koh Kong and Siem Reap Provinces;
from Vietnam: Lam Dong, Dak Lak, and Dak Nong Provinces;
from China: Guangxi Province;
from Vietnam: Ninh Thuan Province;
from Vietnam: Dong Nai and Ninh Thuan Provinces; and
from China: Yunnan Province. All newly described species are morphologically described, illustrated, and molecularly compared to congenerics. With the molecular results revealing cryptic taxa, it was found necessary for
(Wood-Mason, 1875),
to have a neotype specimen designated to allow accurate differentiation from congenerics. To conclude, male and female dichotomous keys to species for the
are presented.
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