Species and speciation.

This chapter discusses two species models, which are diametrically opposed. The first, often called the 'biological species concept', defines species in terms of 'reproductive isolation', convinced that species arise when subsets of a population are split off and remain geographically isolated over evolutionary time. If and when such new species are reunited with their founder population, interbreeding does not occur, or if it does, infertile progeny result. Hence, from the biological species concept, natural selection is a primary agent of change and directly selects for new species. In this sense, species are the direct products of natural selection and they are therefore 'adaptive devices'. When applying this species concept, it has been impossible to separate some sibling species of fruit flies in the genus Bactrocera where distinct morphological species can be similar in molecular analyses of certain DNA sequences, while similar species morphologically are distinct in the same molecular characters. A radically different model, the 'recognition concept of species', relies heavily on a knowledge of species ecology and behaviour, particularly in their natural habitat. The principal points in this concept are given. In contrast to the now-outdated biological species concept that leads one to depend on laboratory-based research to define species, the recognition concept requires workers to undertake extensive field research in the habitat of the taxon under investigation. In translating this approach to research in the insect family Tephritidae, particularly the Dacinae, some 35 years of field surveys have been undertaken throughout the Indian subcontinent, South-east Asia and the South Pacific region. These surveys included trapping using male lure traps and host fruit collections of commercial/edible fruits. The results of this work have included the provision of specimens of almost all known species for morphological descriptions (c.800 species), material for male pheromone chemistry, and data on host fruit relationships and biogeographical studies.

Validity of Pampus liuorum Liu & Li, 2013, Revealed by the DNA Barcoding of Pampus Fishes (Perciformes, Stromateidae)

The genus Pampus contains seven valid species, which are commercially important fishery species in the Indo-Pacific area. Due to their highly similar external morphologies, Pampus liuorum has been proposed as a synonym of Pampus cinereus. In this study, partial sequences of COI (582 bp) and Cytb (1077 bp) were presented as potential DNA barcodes of six valid Pampus species and the controversial species P. liuorum. A species delimitation of the seven Pampus species was performed to verify their validities. Explicit COI barcoding gaps were found in all assessed species, except for P. liuorum and P. cinereus, which resulted from their smaller interspecific K2P distance (0.0034–0.0069). A Cytb barcoding gap (0.0200) of the two species was revealed, with a K2P distance ranging from 0.0237 to 0.0277. The longer Cytb fragment is thus a more suitable DNA barcode for the genus Pampus. In the genetic tree, using concatenated Cytb and COI sequences, the seven species reciprocally formed well-supported clades. Species delimitations with ABGD, GMYC, and bPTP models identified seven operational taxonomic units, which were congruent with the seven morphological species. Therefore, all of the seven analyzed species, including P. liuorum, should be kept as valid species.

Assessing the Value of a Citizen Science Approach for Ctenophore Identification

During the era of biodiversity loss, a complete species census and understanding where the different species occur is of high priority. Even though this knowledge has increased tremendously, mainly with expanded use of integrated taxonomic identification, there are groups where our knowledge is very limited, both in terms of diversity and distribution. Ctenophores are such a group. Due to a lack of identification literature, damage to specimens during net sampling and sample processing, difficulties with preservation and a considerably undescribed diversity within the phylum, this group is often hard to work with. A citizen science approach was applied during a mapping campaign on ctenophore diversity along the Norwegian coast in order to have a broad geographical coverage. This was achieved by a collaboration with five diving clubs along a south-north geographical gradient that were briefly introduced to ctenophore taxonomy and ecology and sampling techniques using Whatman® FTA® Cards. The data collected by the participating divers gave a broad spatial coverage and provided information on ctenophore diversity in these regions. The use of FTA® Cards in the sampling allowed successful species and genus level identification using DNA barcodes. However, small obstacles such as accurate morphological species identification and labor-intensive issues were identified that can impede the use of large-scale citizen science approaches to map ctenophore diversity and thus recommendations for future implications that address these issues are proposed here.

Specifics of the morphological identification of the pathogen of passaluariasis of rabbits

Passalurus ambiguus (Nematoda, Oxyuroidae) is one of the most common parasites of digestive tract of domestic and wild rabbits and rodents. Passalurus spp. are cosmopolitan, and the mature nematodes are localized in the appendages and large intestine of animals. The passaluariasis infections remain quite relevant in modern rabbit breeding, because the disease is highly contagious, with the possibility of unlimited spread inducing significant economic losses. The aim of the study was to determine the identifying morphological species characteristics of P. ambiguus nematodes, which were isolated from the colon of domestic rabbits (Oryctolagus cuniculus domesticus). The identifying characters of Passalurus include morphological features, namely the presence of a spherical bulb in the esophagus, and the presence of three teeth in the oral capsule. Males of P. ambiguus have a characteristic structure of the tail end, namely the presence of papillary protrusions and a massive narrowed part with a spicule handle, and five papillae around the cloaca. Twenty-eight metric indicators are proposed that characterize the size of the body, oral capsule, esophagus in different parts of it, the tail end, spicules, the location of the cloaca. Two different morphotypes of mature females of P. ambiguus were revealed – short-tailed and long-tailed, which were larger by 19 indicators (by 3.2–43.6%). The morphotypes of P. ambiguus females are characterized; the length of the tail, body length and width in different areas, depth of the oral capsule, esophageal size and its structural elements, the location of the vulva and nerve ring, the width of the caudal process. At the same time, the parameters of esophageal bulb length and caudal process in short-tailed females were higher (by 13.9% and 11.9%, respectively) than in the long-tailed females. A total of 25 morphometric parameters were proposed for the identification of P. ambiguus females. The obtained data indicate the feasibility of further research on the causes of occurrence of such morphotypes in P. ambiguus females and the need to take into account the existence of such forms of females for their differential diagnosis taking into account their proposed morphometric parameters.

Ormyrus labotus Walker (Hymenoptera: Ormyridae): another generalist that should not be a generalist is not a generalist

Several recent reappraisals of supposed generalist parasite species have revealed hidden complexes of species, each with considerably narrower host ranges. Parasitic wasps that attack gall-forming insects on plants have life history strategies that are thought to promote specialization, and though many species are indeed highly specialized, others have been described as generalist parasites. Ormyrus labotus Walker (Hymenoptera: Ormyridae) is one such apparent generalist, with rearing records spanning more than 65 host galls associated with a diverse set of oak tree species and plant tissues. We pair a molecular approach with morphology, host ecology, and phenological data from across a wide geographic sample to test the hypothesis that this supposed generalist is actually a complex of several more specialized species, though we identify no single unifying axis of specialization. We find 16-18 putative species within the morphological species O. labotus, each reared from only 1-6 host gall types. We also find cryptic habitat specialists within two other named Ormyrus species. Our study suggests that caution should be applied when considering host ranges of parasitic insects described solely by morphological traits, particularly given their importance as biocontrol organisms and their role in biodiversity and evolutionary studies.

Shallow-water Sponges from a High-sedimentation Estuarine Bay (Brunei, Northwest Borneo, Southeast Asia)

Tropical estuaries are important habitats for invertebrates including sponges, a group of marine organisms that fulfill significant ecological roles and provide ecosystem services. Here, we describe the sponge fauna from Pulau Bedukang, a small island in a turbid, variable salinity, acidified and eutrophic estuarine bay (Brunei Darussalam, northwest Borneo). We present records for 14 morphological species (OTUs). Six of these species belong to the Haplosclerida, an order of shallow-water sponges that usually tolerate more variable and extreme physical conditions. Our baseline data contribute to the regional biogeography of sponges and present a reference source for ecological studies on marine animals inhabiting variable estuarine environments. This is the first known record of sponges from the northwest Bornean region of the South China Sea that are not associated with a coral ecosystem; other studies have concerned Singapore, peninsular Malaysia, Thailand, Cambodia, Vietnam, southern China, and Taiwan.

Revision of the Exechia parva group (Diptera: Mycetophilidae)

Exechia is a diverse genus of small fungus gnats, widespread in the Holarctic Region, while the fauna is largely unknown elsewhere, such as in the Afrotropical and Oriental Region. Members of Exechia can be arranged into several species groups, based on homologies in the male and female terminalia. The Exechia parva group is delimited, based on male terminalia possessing a pair of gonocoxal lobes on the apicoventral gonocoxal margin. Eight previously-described species can be placed in this group, of which six are from the Holarctic Region, while one is recorded each from the Oriental and the Afrotropical Regions. The Exechia parva group was reviewed and found to include 33 species, of which 24 were described as new to science and six were re-described. Identification keys to 32 species for males and nine species for females are provided together with illustrations and photos of male and female terminalia. Species delimitations were based on morphological examination of 94 male and female specimens, as well as DNA barcodes obtained from 124 specimens. Molecular and morphological species delimitations were mostly congruent, except in two cases where two species were delimited within a single Barcode Index Number (BIN). We found that each species is only known from a single zoogeographical region and that several species complexes are largely congruent with zoogeographical divisions, indicating that intercontinental barriers may have a strong impact on the species diversity of the group.

DNA-based taxonomy of a mangrove-associated community of fishes in Southeast Asia

The Merbok Estuary comprises one of the largest remaining mangrove forests in Peninsular Malaysia. Its value is significant as it provides important services to local and global communities. It also offers a unique opportunity to study the structure and functioning of mangrove ecosystems. However, its biodiversity is still partially inventoried, limiting its research value. A recent checklist based on morphological examination, reported 138 fish species residing, frequenting or subject to entering the Merbok Estuary. In this work, we reassessed the fish diversity of the Merbok Estuary by DNA barcoding 350 specimens assignable to 134 species initially identified based on morphology. Our results consistently revealed the presence of 139 Molecular Operational Taxonomic Units (MOTUs). 123 of them are congruent with morphology-based species delimitation (one species = one MOTU). In two cases, two morphological species share the same MOTU (two species = one MOTU), while we unveiled cryptic diversity (i.e. COI-based genetic variability > 2%) within seven other species (one species = two MOTUs), calling for further taxonomic investigations. This study provides a comprehensive core-list of fish taxa in Merbok Estuary, demonstrating the advantages of combining morphological and molecular evidence to describe diverse but still poorly studied tropical fish communities. It also delivers a large DNA reference collection for brackish fishes occurring in this region which will facilitate further biodiversity-oriented research studies and management activities.

Cryptic diversity and gene introgression of Moinidae (Crustacea: Cladocera) in Nigeria

The distribution and species/lineage diversity of freshwater invertebrate zooplankton is understudied in Sub-Saharan Africa. In the present study, we explored the lineage diversity and regional distribution of Moinidae (Crustacea: Cladocera) species in Southeast Nigeria. Three species of Moinidae were identified, based on morphology, in 11 of 32 Nigerian lakes examined. Their phylogenetic relationships were investigated based on mitochondrial dna sequences (cytochrome oxidase c subunit I gene; coi) and two nuclear internal transcribed spacer regions (its-1 and its-2). Three coi lineages were detected, corresponding to the morphological species. Two of the coi lineages are newly reported, but one coi lineage (and the haplotype found) is globally distributed, suggesting an ability of moinids to disperse over long distances. Interestingly, two individuals that were morphologically M. cf. macrocopa and had its alleles typical of that species had mtDNA sequences typical of M. cf. micrura. Additionally, one individual that corresponded morphologically to M. cf. macrocopa (and also had a mitochondrial sequence typical of M. cf. micrura) had one its-2 allele typical of that species and one typical of M. cf. micrura. This discordance between mtDNA and nuclear phylogenies suggests gene introgression and/or hybridization between different species within the genus. Our data shows the lineage distribution/diversity and the presence of gene introgression/interspecific hybridization among moinid species from a tropical region.