DNA barcodes for the pipefish genus Corythoichthys (Actinopterygii: Syngnathiformes) from the Indian Ocean provide insights into cryptic diversity

The syngnathiform genus Corythoichthys comprises a group of taxonomically complex, tail-brooding (Syngnathinae) pipefishes widely distributed in the Indo-Pacific region. Due to the presence of overlapping interspecific morphological characters, reliable taxonomic information on Corythoichthys is still lacking. Using 52 CO1 sequences, including seven newly generated, a phylogenetic analysis was carried out to understand the genetic diversity, distribution and ‘species groups’ within the genus Corythoichthys. Species delimitation using Automatic Barcode Gap Discovery (ABGD) analysis confirmed the presence of 13 species which include ‘species-complexes’ previously considered as a single taxon. Our results revealed the presence of three species groups, ‘C. amplexus’, ‘C. conspicillatus’ and ‘C. haematopterus’ and four unidentified/undescribed species in the wider Indo-Pacific realm. Interestingly, 60 sequences and a mitogenome identified as Corythoichthys in GenBank are misidentified at the genus level. Based on our findings, we suggest that the taxonomy and systematics of Corythoichthys need to be re-examined and validated using integrative methods, and care should be taken while selecting specimens for genetic studies.     

Micro‐evolutionary diversification among Indian Ocean parrots: temporal and spatial changes in phylogenetic diversity as a consequence of extinction and invasion

Almost 90% of global bird extinctions have occurred on islands. The loss of endemic species from island systems can dramatically alter evolutionary trajectories of insular species biodiversity, resulting in a loss of evolutionary diversity important for species adaptation to changing environments. The Western Indian Ocean islands have been the scene of evolution for a large number of endemic parrots. Since their discovery in the 16th century, many of these parrots have become extinct or have declined in numbers. Alongside the extinction of species, a number of the Indian Ocean islands have experienced colonization by highly invasive parrots, such as the Ring‐necked Parakeet Psittacula krameri. Such extinctions and invasions can, on an evolutionary timescale, drive changes in species composition, genetic diversity and turnover in phylogenetic diversity, all of which can have important impacts on species potential for adaptation to changing environmental and climatic conditions. Using mtDNA cytochrome b data, we resolve the taxonomic placement of three extinct Indian Ocean parrots: the Rodrigues Psittacula exsul, Seychelles Psittacula wardi and Reunion Parakeets Psittacula eques. This case study quantifies how the extinction of these species has resulted in lost historical endemic phylogenetic diversity and reduced levels of species richness, and illustrates how it is being replaced by non‐endemic invasive forms such as the Ring‐necked Parakeet. Finally, we use our phylogenetic framework to identify and recommend a number of phylogenetically appropriate ecological replacements for the extinct parrots. Such replacements may be introduced once invasive forms have been cleared, to rejuvenate ecosystem function and restore lost phylogenetic diversity.     

Assessing the diversity and distribution of Cephalothrix species (Nemertea: Palaeonemertea) in European waters by comparing different species delimitation methods

Soft‐bodied marine taxa, like ribbon worms (Nemertea), often lack clear diagnostic morphological characters impeding traditional species delimitation. Therefore, recent studies concentrated on molecular genetic methods to solve taxonomic issues. Different delimitation methods were employed to explore species boundaries and the presence of cryptic species. However, the performance of the different delimitation methods needs to be tested. A particularly promising nemertean genus in this regard is the palaeonemertean genus Cephalothrix that is commonly found in European waters. In order to gain information on the number and distribution of European cephalotrichids and to test different tree‐based and non‐tree‐based delimitation methods, we analyzed a dataset comprising the barcoding region of the mitochondrial cytochrome c oxidase subunit I (COI) of 215 European Cephalothrix specimens, of which 78 were collected for this study. Our results show the presence of 12–13 European lineages of which several can be assigned to known European species. Analyzing a second dataset comprising 74 additional sequences from the Pacific and the Atlantic Oceans helped identify some of the unassigned European specimens. One resulting clade seems to represent a non‐native introduced Cephalothrix species, while another has never been recorded from Europe before. In our analysis, especially the tree‐based methods and the phylogenetic analysis proved to be a useful tool when delimiting species. It remains unclear whether the different identified clades result from cryptic speciation or from a high genetic variability of the COI gene.     

Evolutionary systematics of the Australian Cyzicidae (Crustacea,Branchiopoda, Spinicaudata) with the description of a new genus

In Australia's arid and semi‐arid zone, most aquatic habitats are nonpermanent. Although approximately 70% of its land surface belongs to these zones, very little is known of the iconic ‘large branchiopods’ that inhabit these important and widespread habitats. In the present study, we investigated 737 Australian specimens of the spinicaudatan taxa Caenestheria and Caenestheriella with a combination of one mitochondrial (cytochrome oxidase subunit I; COI) and three nuclear (elongation factor 1α, internal transcribed spacer 2, and 28S) markers to assess the diversity of species, their phylogenetic relationships, and phylogeographical history. The initial species delimitation was based on COI employing a combination of phylogenetic analyses and two automated approaches to species delimitation (general mixed Yule coalescent model and Automated Barcode Gap Discovery). The outcome was tested by the nuclear markers and considered under differing species concepts. The number of delineated species ranged from 14–27, in no case being in full agreement with any of the two automated approaches. The lower numbers resulted if inferred reproductive isolation, as required for the biological or Hennigian species concept, was employed. Although nuclear markers did not indicate ongoing reproduction, the lack of sympatric co‐occurrences inhibited inferences of definitive reproductive isolation in several instances. If monophyly or an ‘independent evolutionary fate’ was employed, as required for the phylogenetic or evolutionary species concepts, the species' distribution was of no importance and up to 27 species could be delimitated. Because the Australian representatives of both studied genera could not be clearly separated from each other but constitute a single monophyletic clade separated from all available non‐Australian representatives of these genera, we describe a new spinicaudatan genus Ozestheria gen. nov. to accommodate these species. Populations revealed relatively small levels of genetic differentiation over large areas of central and eastern Australia. By far the most pronounced levels of genetic differentiation were observed towards the north‐eastern regions, a pattern possibly explainable by ecological conditions and the movement of nomadic water birds that disperse resting eggs. © 2015 The Linnean Society of London     

Evidence for evolutionary distinctiveness of a newly discovered population of sooglossid frogs on Praslin Island, Seychelles

Amidst a worldwide decline in amphibian populations, those species endemic to islands remain an important focus for conservation efforts. The Sooglossidae are a family of frog species endemic to the Seychelles islands that are believed to have evolved in isolation for approximately 75 million years. Formerly thought to inhabit just two Seychelles islands (Mahé and Silhouette), a third population was discovered on Praslin in 2009. Phylogenetic analysis based on 438 bp of mitochondrial 16S rRNA suggests that the Praslin population is most closely related to Sooglossus sechellensis from Silhouette, and identifies these as two separate clades which together sit distinct from the population on Mahé. An average of 4.06% uncorrected pairwise sequence divergence between the Praslin and Silhouette populations suggests substantial evolutionary divergence rather than recent introduction. Discriminant function analysis also revealed differences in morphology in frogs from Praslin and Mahé. DNA sequences of two Praslin specimens group more closely with the Mahé population, indicating some shared haplotypes that suggest recent secondary contact. Tests for a genetic signature of recent population expansion on either island were not significant. Our results suggest substantial evolutionary divergence between the three populations of S. sechellensis, most likely following isolation due to changes in sea level in the Indian Ocean. Whilst further genetic sampling and ecological studies are needed, our initial phylogenetic analyses suggest that the sooglossid population on Praslin should be managed as an evolutionarily significant unit to retain the uniqueness of its genetic diversity and its evolutionary trajectory within this ancient family of amphibians.     

A new species, Parupeneus procerigena, from the Saya de Malha Bank in the western Indian Ocean (Perciformes: Mullidae)

A new mullid fish, Parupeneus procerigena, is described on the basis of 13 specimens (118.9–198.4 mm SL) from depths of 92–148 m off the Saya de Malha Bank in the western Indian Ocean. This species resembles P. chrysopleuron and P. heptacanthus in color pattern without black stripes or spots, but it differs from them in having more gill rakers, two scales in lachrymal region, deeper body, deeper cheek, and longer distance between nostrils. Received: April 4, 2000 / Revised: July 27, 2000 / Accepted: August 27, 2000     

Species delimitation and phylogeographic analyses in the Ectocarpus subgroup siliculosi (Ectocarpales,Phaeophyceae)

The genus Ectocarpus (Ectocarpales, Phaeophyceae) contains filamentous algae widely distributed in marine and estuarine habitats of temperate regions in both hemispheres. While E. siliculosus has become a model organism for genomics and genetics of the brown macroalgae, accurate species delineation, distribution patterns and diversity for the genus Ectocarpus remain problematic. In this study, we used three independent species delimitation approaches to generate a robust species hypothesis for 729 Ectocarpus specimens collected mainly along the European and Chilean coasts. These approaches comprised phylogenetic reconstructions and two bioinformatics tools developed to objectively define species boundaries (General Mixed Yule Coalescence Method and Automatic Barcode Gap Discovery). Our analyses were based on DNA sequences of two loci: the mitochondrial cytochrome oxidase subunit 1 and the nuclear internal transcribed spacer 1 of the ribosomal DNA. Our analyses showed the presence of at least 15 cryptic species and suggest the existence of incomplete lineage sorting or introgression between five of them. These results suggested the possible existence of different levels of reproductive barriers within this species complex. We also detected differences among species in their phylogeographic patterns, range and depth distributions, which may suggest different biogeographic histories (e.g., endemic species or recent introductions).     

Issue Information

Aeolidia papillosa (Linnaeus, 1761 ) is a well‐known aeolidiid species that has been reported to have a worldwide distribution in cold–temperate waters, mainly from the northern hemisphere. Molecular tools have recently shown that most cosmopolitan species usually belong to a taxonomic species complex. Here we used integrative taxonomy to test the range of distribution of A. papillosa, and to assess the existence of a putative species complex that has been traditionally included as a single species under the name A. papillosa. Maximum‐likelihood and Bayesian analyses of partial DNA sequences of the mitochondrial cytochrome c oxidase subunit I and 16S rRNA genes, and the nuclear gene histone 3, were used to infer phylogenetic trees. Automatic Barcode Gap Discovery (ABGD) species delimitation analyses and morphological study complemented the phylogenetic approach. Our results show that A. papillosa is a cosmopolitan and an amphi‐Atlantic species, being distributed in the eastern and western Atlantic as well as in the eastern Pacific; however, some specimens from the UK and the Netherlands, together with specimens from Portugal, Galicia, and France, as well as the Californian and Oregon populations, emerge as two pseudocryptic species described herein: Aeolidia filomenae  sp. nov. and Aeolidia loui  sp. nov. , respectively. Finally, the specimens from Chilean coasts, previously attributed to A. papillosa, belong to a different species, Aeolidia campbellii (Cunningham, 1871 ), that is a senior synonym of Aeolidia serotina Bergh, 1873 .     

Species diversity of the genus Osmundea (Ceramiales,Rhodophyta) in the Macaronesian region

Species diversity within the genus Osmundea in the Macaronesian region was explored by conducting a comprehensive sampling in the Azores, the Canary, and the Madeira archipelagos. Toward identification, all specimens were first observed alive to verify the absence of corps en cerise, a diagnostic character for the genus and morphometric data were measured (thallus length and width, first‐order branches length and width, branchlets length and width, cortical cell length and width in surface view, cortical cell length and width in transverse section). Specimens were sequenced for COI‐5P (39 specimens) and three species delimitation methods (Generalized Mixed Yule Coalescent, Automatic Barcode Gap Discovery method, and Poisson Tree Processes) were used to assess the threshold between infra‐ and interspecific relationships. Subsequently, one or several sequences of plastid‐encoded large subunit of RuBisCO (21 specimens) per delimited species were generated to assess the phylogenetic relationships among Macaronesian Osmundea. Moreover, for each delineated species, vegetative and reproductive anatomy was thoroughly documented and, when possible, specimens were either assigned to existing taxa or described as novel species. This integrative approach has provided data for (i) the presence of O. oederi, O. pinnatifida, and O. truncata in Macaronesia; (ii) the proposal of two novel species, O. prudhommevanreinei sp. nov. and O. silvae sp. nov.; and (iii) evidence of an additional species referred as “Osmundea sp.1,” which is a sister taxon of O. hybrida.     

Integrative taxonomy of the Clavus canalicularis species complex (Drilliidae,Conoidea, Gastropoda) with description of four new species

ABSTRACT

The conoidean family Drilliidae Olsson, 1964 is a species-rich lineage of marine gastropods, showing a high degree of diversification in comparison to other families of Conoidea. Despite intensive molecular phylogenetic studies during the last decade that have led to notable rearrangements of conoidean systematics, the genus- and species-level taxonomy of Drilliidae has not thus far been affected and remains entirely based on shell features. In the current study we revisit species delimitation in a morphological cluster of species from the Indo-Pacific referred to as the Clavus canalicularis complex, using an integrative taxonomy approach. The species in the complex possess robust thick-walled shells typically over 15?mm in height with sculpture of prominent rounded nodules located at the whorl’s shoulder, sometimes sharp and squamiform, or producing long spines. We find that in addition to five known species, the complex comprises four new species. These are described as Clavus brianmayi n. sp. (New Caledonia), Clavus davidgilmouri n. sp. (the Philippines), Clavus andreolbrichi n. sp. (Vanuatu and New Ireland) and Clavus kirkhammetti n. sp. (Madagascar). Clavus exasperatus (Reeve, 1843), which was previously considered widely distributed in Indo-Pacific, is shown to be confined to the western Indian Ocean.     

Single-locus DNA barcoding and species delimitation of the sandfly subgenus Evandromyia (Aldamyia)

Sandfly specimens from the subgenus Evandromyia (Aldamyia) Galati, 2003 (Diptera: Psychodidae: Phlebotominae) were collected between 2012 and 2019 from nine localities in seven Brazilian states, morphologically-identified, and then DNA barcoded by sequencing the mitochondrial cytochrome c oxidase subunit I (coi) gene. Forty-four new barcode sequences generated from 10 morphospecies were combined with 49 previously published sequences from the same subgenus and analysed using sequence-similarity methods (best-match criteria) to assess their ability at specimen identification, while four different species delimitation methods (ABGD, GMYC, PTP and TCS) were used to infer molecular operational taxonomic units (MOTUs). Overall, seven of the 11 morphospecies analysed were congruent with both the well-supported clades identified by phylogenetic analysis and the MOTUs inferred by species delimitation, while the remaining four morphospecies – E. carmelinoi, E. evandroi, E. lenti and E. piperiformis – were merged into a single well-supported clade/MOTU. Although E. carmelinoi, E. evandroi and E. lenti were indistinguishable using coi DNA barcodes, E. piperiformis did form a distinct phylogenetic cluster and could be correctly identified using best-match criteria. Despite their apparent morphological differences, we propose on the basis of the molecular similarity of their DNA barcodes that these latter four morphospecies should be considered members of a recently-diverged species complex.     

A phylogenetic analysis of the palm subtribe Oncospermatinae (Arecaceae) based on morphological characters

Subtribe Oncospermatinae (Arecaceae: Arecoideae: Areceae) is a diverse group of spiny Old World palms. The subtribe includesOncosperma, a widespread Asian genus of five species, along with seven monotypic genera, all endemic to the Seychelles and Mascarene Islands of the western Indian Ocean. A phylogenetic analysis was conducted in order to test the monophyly of subtribe Oncospermatinae with respect to other Old World genera of tribe Areceae. A matrix of 38 morphological characters was scored for 29 taxa, including 11 species of the Oncospermatinae. A single most parsimonious tree was found, resolving the subtribe as a polyphyletic group of two distinct clades. One clade containingAcanthophoenix, Deckenia, Oncosperma, andTectiphiala was placed as sister to a large group that includes members of subtribes Archontophoenicinae, Arecinae, Iguanurinae, and Ptychospermatinae. The other clade of Oncospermatinae, including the Seychelles endemic generaNephrosperma, Phoenicophorium, Roscheria, andVerschaffeltia, was resolved as sister to the Madagascar endemic subtribe Masoalinae, and may have arisen in the western Indian Ocean region.     

Embryonic development of the false limpet Siphonaria lateralis from Atlantic Patagonia

Siphonariids are pulmonate gastropods inhabiting rocky intertidal habitats, and many studies have focused on these false limpets around the world. In the southern South Atlantic, studies on reproduction and development in species of Siphonaria are scarce. We studied the embryonic development and egg masses of Siphonaria lateralis at its northernmost distribution in Atlantic Patagonia. In S. lateralis, as in most species of Siphonaria, individuals spawn benthic egg masses that strongly attach to intertidal rocky substrata. A single spherical egg that measures ~120 µm develops inside the egg capsule of S. lateralis. Considering the relatively small egg size, and reports from previous studies, the developmental modality of S. lateralis might be expected to include a planktotrophic larval phase. However, we found that hatchlings emerged as 1‐mm crawling juveniles, probably owing to the presence of intracapsular fluid, which may provide the energetic requirements for direct development. The embryonic size changed little from the egg to veliger stages, and then increased rapidly until the hatchling stage. We compared development in S. lateralis with development in the sympatric Siphonaria lessonii, in which egg size was reported to be ~80 µm and hatching occurs as planktotrophic veliger larvae. In these two species, spawn and early intracapsular developmental modes are remarkably different; these differences represent contrasting ways to survive in the harsh and physically stressful intertidal Patagonian coasts.     

Eastward from Africa: palaeocurrent-mediated chameleon dispersal to the Seychelles islands

Madagascar and the Seychelles are Gondwanan remnants currently isolated in the Indian Ocean. In the Late Cretaceous, these islands were joined with India to form the Indigascar landmass, which itself then split into its three component parts around the start of the Tertiary. This history is reflected in the biota of the Seychelles, which appears to contain examples of both vicariance- and dispersal-mediated divergence from Malagasy or Indian sister taxa. One lineage for which this has been assumed but never thoroughly tested is the Seychellean tiger chameleon, a species assigned to the otherwise Madagascar-endemic genus Calumma. We present a multi-locus phylogenetic study of chameleons, and find that the Seychellean species is actually the sister taxon of a southern African clade and requires accomodation in its own genus as Archaius tigris. Divergence dating and biogeographic analyses indicate an origin by transoceanic dispersal from Africa to the Seychelles in the Eocene–Oligocene, providing, to our knowledge, the first such well-documented example and supporting novel palaeocurrent reconstructions.     

Phylogeny and species reassessment of Hyalopterus (Aphididae,Aphidinae)

The broadly distributed genus Hyalopterus currently comprises three formally recognized species that are highly similar morphologically and hence difficult to be identified with certainty. This group has undergone multiple revisions in the past century, but none of these has assessed species from Asia, which has hampered our understanding of the species diversity within this genus. Based on a comprehensive data set from morphological data and host-associated data, and by coalescent-based delimitation approaches, the Hyalopterus species boundaries, distribution and diversity were clarified here to further reveal the composition of the species. Two single-locus (ML-GMYC and mPTP) and two multilocus (BPP and STACEY) delimitation methods were conducted based on extensive sampling. Then, the phylogenetic relationships and morphological divergence were assessed. Our data strongly supported that the number of recognized species in Hyalopterus had likely been underestimated. The phylogenetic analyses recovered four major clades, which corresponded to distinct host-plant preferences. Also, the morphological analyses showed significant differentiation for only one of the newly recognized candidate species uncovered by the delimitation approaches, suggesting the existence of at least two independent evolutionary lineages within Hyalopterus arundiniformis, which showed different patterns of host association. Moreover, based on our data, the taxonomic misidentification of H. arundiniformis in China was corrected here. This study lays the groundwork for the thorough taxonomic revision of Hyalopterus and for future evolutionary studies and underlines the importance of an integrated framework for species determination.     

Are the native giant tortoises from the Seychelles really extinct? A genetic perspective based on mtDNA and microsatellite data

The extinction of the giant tortoises of the Seychelles Archipelago has long been suspected but is not beyond doubt. A recent morphological study of the giant tortoises of the western Indian Ocean concluded that specimens of two native Seychelles species survive in captivity today alongside giant tortoises of Aldabra, which are numerous in zoos as well as in the wild. This claim has been controversial because some of the morphological characters used to identify these species, several measures of carapace morphology, are reputed to be quite sensitive to captive conditions. Nonetheless, the potential survival of giant tortoise species previously thought extinct presents an exciting scenario for conservation. We used mitochondrial DNA sequences and nuclear microsatellites to examine the validity of the rediscovered species of Seychelles giant tortoises. Our results indicate that the morphotypes suspected to represent Seychelles species do not show levels of variation and genetic structuring consistent with long periods of reproductive isolation. We found no variation in the mitochondrial control region among 55 individuals examined and no genetic structuring in eight microsatellite loci, pointing to the survival of just a single lineage of Indian Ocean tortoises.     

Phylogeny and species delimitation of the C‐genome diploid species in Oryza

Abstract The diploid Oryza species with C‐genome type possesses abundant genes useful for rice improvement and provides parental donors of many tetraploid species with the C‐genome (BBCC, CCDD). Despite extensive studies, the phylogenetic relationship among the C‐genome species and the taxonomic status of some taxa remain controversial. In this study, we reconstructed the phylogeny of three diploid species with C‐genome (Oryza officinalis, O. rhizomatis, and O. eichingeri) based on sequences of 68 nuclear single‐copy genes. We obtained a fully resolved phylogenetic tree, clearly indicating the sister relationship of O. officinalis and O. rhizomatis, with O. eichingeri being the more divergent lineage. Incongruent phylogenies of the C‐genome species found in previous studies might result from lineage sorting, introgression/hybridization and limited number of genetic markers used. We further applied a recently developed Bayesian species delimitation method to investigate the species status of the Sri Lankan and African O. eichingeri. Analyses of two datasets (68 genes with a single sample, and 10 genes with multiple samples) support the distinct species status of the Sri Lankan and African O. eichingeri. In addition, we evaluated the impact of the number of sampled individuals and loci on species delimitation. Our simulation suggests that sampling multiple individuals is critically important for species delimitation, particularly for closely related species.     

An introduced population of Chorda asiatica (Chordaceae,Laminariales) in Puget Sound,Pacific coast of North America

Northeastern Pacific Ocean and northwestern Atlantic Ocean populations of Chorda species, which have not been examined in previous phylogenetic studies, were investigated. All specimens that were collected in Hood Canal, Puget Sound, WA, USA, Pacific coast of North America, showed identical ITS‐5.8S rDNA sequences, and they were included in the clade of Japanese Chorda asiatica. With morphological data added to the molecular data, they were identified as C. asiatica and were concluded to be non‐indigenous populations, most likely introduced with oyster spat together with Sargassum muticum. Specimens collected in New York, NY, USA, Atlantic coast of North America, were genetically closest to C. filum from Newfoundland and were identified as C. filum. The genetic divergence of the North Atlantic populations of C. filum was relatively small compared to that of Japanese C. asiatica considering their broader distributional ranges on both sides of the Atlantic.