Advances In Molecular Systematics Research Articles

The CAM lineages of planet Earth.

The growth of experimental studies of crassulacean acid metabolism (CAM) in diverse plant clades, coupled with recent advances in molecular systematics, presents an opportunity to re-assess the phylogenetic distribution and diversity of species capable of CAM. It has been more than two decades since the last comprehensive lists of CAM taxa were published, and an updated survey of the occurrence and distribution of CAM taxa is needed to facilitate and guide future CAM research. We aimed to survey the phylogenetic distribution of these taxa, their diverse morphology, physiology and ecology, and the likely number of evolutionary origins of CAM based on currently known lineages. We found direct evidence (in the form of experimental or field observations of gas exchange, day-night fluctuations in organic acids, carbon isotope ratios and enzymatic activity) for CAM in 370 genera of vascular plants, representing 38 families. Further assumptions about the frequency of CAM species in CAM clades and the distribution of CAM in the Cactaceae and Crassulaceae bring the currently estimated number of CAM-capable species to nearly 7 % of all vascular plants. The phylogenetic distribution of these taxa suggests a minimum of 66 independent origins of CAM in vascular plants, possibly with dozens more. To achieve further insight into CAM origins, there is a need for more extensive and systematic surveys of previously unstudied lineages, particularly in living material to identify low-level CAM activity, and for denser sampling to increase phylogenetic resolution in CAM-evolving clades. This should allow further progress in understanding the functional significance of this pathway by integration with studies on the evolution and genomics of CAM in its many forms.

Updating splits, lumps, and shuffles: Reconciling GenBank names with standardized avian taxonomies

Abstract Biodiversity research has advanced by testing expectations of ecological and evolutionary hypotheses through the linking of large-scale genetic, distributional, and trait datasets. The rise of molecular systematics over the past 30 years has resulted in a wealth of DNA sequences from around the globe. Yet, advances in molecular systematics also have created taxonomic instability, as new estimates of evolutionary relationships and interpretations of species limits have required widespread scientific name changes. Taxonomic instability, colloquially “splits, lumps, and shuffles,” presents logistical challenges to large-scale biodiversity research because (1) the same species or sets of populations may be listed under different names in different data sources, or (2) the same name may apply to different sets of populations representing different taxonomic concepts. Consequently, distributional and trait data are often difficult to link directly to primary DNA sequence data without extensive and time-consuming curation. Here, we present RANT: Reconciliation of Avian NCBI Taxonomy. RANT applies taxonomic reconciliation to standardize avian taxon names in use in NCBI GenBank, a primary source of genetic data, to a widely used and regularly updated avian taxonomy: eBird/Clements. Of 14,341 avian species/subspecies names in GenBank, 11,031 directly matched an eBird/Clements; these link to more than 6 million nucleotide sequences. For the remaining unmatched avian names in GenBank, we used Avibase’s system of taxonomic concepts, taxonomic descriptions in Cornell’s Birds of the World, and DNA sequence metadata to identify corresponding eBird/Clements names. Reconciled names linked to more than 600,000 nucleotide sequences, ~9% of all avian sequences on GenBank. Nearly 10% of eBird/Clements names had nucleotide sequences listed under 2 or more GenBank names. Our taxonomic reconciliation is a first step towards rigorous and open-source curation of avian GenBank sequences and is available at GitHub, where it can be updated to correspond to future annual eBird/Clements taxonomic updates.

Perizomini (Lepidoptera: Geometridae: Larentiinae) are polyphyletic

Recent advances in molecular systematics have led to an emerging understanding of the phylogenetic history of the family Geometridae. These studies have basically confirmed the traditional subdivision of the subfamily Larentiinae into tribes but unsolved problems remain. Here we test the monophyly of the tribe Perizomini, and evaluate the division of this tribe into genera using Bayesian and maximum likelihood analyses of one mitochondrial and eight nuclear gene fragments. We show that the Eurasian members of Perizoma Hübner, 1825, Mesotype Hübner, 1825 and Gagitodes Warren, 1893 together form a monophyetic tribe Perizomini. However, Martania Mironov, 2000 is not closely related to these genera, but is considered to belong to Melanthiini according to the results of the phylogenetic analyses. Morphological evidence supporting this rearrangement is discussed. The Nearctic Larentia basaliata Walker, 1862 was shown to belong in the genus Martania as M. basaliata (Walker, 1862) comb. nov. and being specifically distinct from the morphologically similar Palaearctic M. taeniata. Three other studied ‘Perizoma’ species from the New World were similarly placed far from Perizomini in the phylogenetic tree, and were not related to each other. We conclude that both the tribe Perizomini and the genus Perizoma are polyphyletic which indicates that the group needs a global revision. It remains an open question whether Perizomini have a worldwide distribution as previously assumed, or is this tribe confined to the Palaearctic region.

Evolution of a sensory cluster on the legs of Opiliones (Arachnida) informs multi-level phylogenetic relationships

AbstractPhylogenetic relationships in Opiliones (Arachnida) at the suborder level have greatly stabilized in recent years, largely due to advances in molecular systematics. Nonetheless, identifying morphological characters in the context of well-resolved phylogenies is essential for testing new systematic hypotheses and establishing diagnostic markers. Here, we investigate with SEM a promising character system across Opiliones: the sensilla on the distalmost article of legs I and II. We identified four discrete characters and scored species of nearly all families of Laniatores (28 families, 44 species), three Dyspnoi, two Eupnoi and two Cyphophthalmi. Using a phylogenetic backbone compiled from recent and ongoing phylogenomic studies, we trace the evolution of these sensilla using ancestral state reconstruction. We discover a widespread occurrence of three sensilla (a pair of sensilla basiconica and one hooded sensillum) on the anterior legs of all families of Laniatores studied, and that comparable structures occur in the other suborders of Opiliones. Our analysis shows that this sensory field provides diagnostic information at different levels of phylogenetic relationships. We discuss the implications of the widespread occurrence of these sensilla in Opiliones, which have recently been hypothesized as hygro-/thermoreceptors and their putative homology with tarsal organs in Arachnida.

Glossing over cryptic species: Descriptions of four new species of Glossodoris and three new species of Doriprismatica (Nudibranchia: Chromodorididae).

Advances in molecular systematics have led to a rapid increase in the identification of cryptic and pseudocryptic species in organisms exhibiting diverse and complex coloration with complicated taxonomic histories. A recent molecular phylogenetic analysis of nudibranchs in the genus Glossodoris (Mollusca: Gastropoda: Heterobranchia: Chromodorididae) and related genera identifies multiple cryptic and pseudocryptic species complexes, one within Glossodoris pallida and three within Glossodoris cincta, and support for three new species of Doriprismatica. Morphological analyses of color pattern, radular structure, buccal mass, and reproductive system support these identifications. Descriptions for Glossodoris buko sp. nov., Glossodoris bonwanga sp. nov., Glossodoris andersonae sp. nov., Glossodoris acosti sp. nov., and what will retain the name Glossodoris sp. cf. cincta are provided here, in addition to descriptions for new species Doriprismatica balut sp. nov., Doriprismatica rossi sp. nov., and Doriprismatica marinae sp. nov.. Glossodoris pallida and G. buko exhibit extreme differences in radular structure in addition to a clear biogeographic split in range. Glossodoris bonwanga, G. andersonae, G. acosti and G. sp. cf. cincta, share morphological and geographic differences but these are not as pronounced as in G. pallida and G. buko. More detailed study of the G. cincta complex is necessary to resolve some remaining systematic challenges. Doriprismatica balut is clearly distinct from all other congeners based on molecular and morphological characters. In contrast, D. rossi and D. marinae are not strongly divergent genetically, but have major morphological divergences that clearly distinguish them.

Advancing the taxonomy of economically important red seaweeds (Rhodophyta)

ABSTRACTThe cultivation of red seaweeds for food (nori), agar and carrageenans is the basis of a valuable industry. However, taxonomic knowledge of these cultivated seaweeds and their wild relatives has not kept pace with advances in molecular systematics despite the fundamental importance of being able to identify commercially important species and strains, discover cryptic and endemic taxa and recognize non-native species with potentially damaging diseases and epiphytes. This review focuses on molecular taxonomic advances in the cultivated red algae with the highest commercial value globally: Eucheuma and Kappaphycus, Porphyra sensu lato and Gracilaria. All three groups are similarly taxonomically challenging: speciose, morphologically plastic, with poorly resolved species boundaries. Eucheuma and Kappaphycus are frequently misidentified and the molecular markers cox2-3 spacer, cox1 and RuBisCO spacer have helped in understanding phylogenetic relationships and identifying new species and haplotypes. In Porphyra sensu lato (Bangiales) species identification and phylogenetic relationships were highly problematic until a taxonomic revision based on a two-gene phylogeny (18S and rbcL) resulted in nine genera of bladed species. Pyropia, with at least 89 species, three in nori cultivation, has potential for new commercial evaluation. In Gracilaria sensu lato, earlier efforts to resolve species-level taxonomy and generic descriptions were superseded by application of molecular tools, including DNA sequences of the RuBisCO spacer, rbcL gene, 18S and the ITS region. Studies of these cultivated red algal genera highlight the need for a robust taxonomy, a more standardized approach to the molecular markers used and a comprehensive dataset for each representative species. Current work on DNA-based species delimitation, the emergence of high throughput sequencing, multi-gene phylogenies, publication of whole genomes (e.g. Porphyra umbilicalis) and genomes in the pipeline (e.g. Gracilaria) are increasingly improving our understanding of phylogenomic relationships and species relationships. This knowledge, in turn, can then be applied to improving red seaweed aquaculture.

Molecular phylogeny of Glossodoris (Ehrenberg, 1831) nudibranchs and related genera reveals cryptic and pseudocryptic species complexes.

Chromodorid nudibranchs (Chromodorididae) are brightly coloured sea slugs that live in some of the most biodiverse and threatened coral reefs on the planet. However, the evolutionary relationships within this family have not been well understood, especially in the genus Glossodoris. Members of Glossodoris have experienced large-scale taxonomic instability over the last century and have been the subject of repeated taxonomic changes, in part due to morphological characters being the sole traditional taxonomic sources of data. Changing concepts of traditional generic boundaries based on morphology also have contributed to this instability. Despite recent advances in molecular systematics, many aspects of chromodorid taxonomy remain poorly understood, particularly at the traditional species and generic levels. In this study, 77 individuals comprising 32 previously defined species were used to build the most robust phylogenetic tree of Glossodoris and related genera using mitochondrial genes cytochrome c oxidase subunit I and 16S, and the nuclear gene 28S. Bayesian inference, maximum likelihood, and maximum parsimony analyses verify the most recent hypothesized evolutionary relationships within Glossodoris. Additionally, a pseudocryptic and cryptic species complex within Glossodoris cincta and a pseudocryptic complex within Glossodoris pallida emerged, and three new species of Doriprismatica are identified.

Experimental taxonomy confirms the environmental stability of morphometric traits in a taxonomically challenging group of microinvertebrates

Despite advances in molecular systematics, the taxonomy of tardigrades still depends largely on morphological and morphometric traits. The fact that the variability of any biological trait is determined by the interaction between genetics and environment prompts a very fundamental question: is it possible for tardigrades of the same genotype, but originating from various habitats that differ in environmental conditions, to have phenotypes so different that they would be erroneously classified as different species taxa by means of classical taxonomy? Here, we present the results of a broad and fully controlled laboratory experiment in which we investigated the phenotypic plasticity of a number of traits that are traditionally considered to be taxonomically important. In order to achieve this, we have cultured six tardigrade species belonging to four eutardigrade families (Milnesiidae, Hypsibiidae, Isohypsibiidae, and Macrobiotidae) under five experimental regimes, reflecting key environmental factors that are likely to vary in natural habitats (i.e. temperature and food availability). We then measured a number of key taxonomic traits and compared their dimensions between the treatments. Over two years of experimentation we have obtained more than 28 000 morphometric measurements for over 2300 individuals. Such an extensive data set allowed us to test some of the fundamental assumptions of classic tardigrade taxonomy. We found that in the five parachelan species analysed, the great majority of both absolute and relative traits differed significantly between the treatments, whereas there were no significant differences in the apochelan species. Overall, tardigrades grew largest under the low-temperature treatment, whereas the smallest specimens were observed under high-temperature and low-food regimes. However, the prevalent statistical significance resulted mainly from the considerable statistical power of our analyses, and not from effect sizes, which varied mostly between low and moderate. In other words, the differences, although consistent, were minor in terms of taxonomical significance, and probably would not be considered by classic taxonomists as sufficient to designate animals from different treatments as separate taxa.

Phylogeny of the subfamilyLarentiinae (Lepidoptera:Geometridae): integrating molecular data and traditional classifications

AbstractLarentiinae are the second largest subfamily ofGeometridae, with more than 6200 described species. Despite recent advances in molecular systematics of geometrid moths, phylogenetic relationships between the numerous subgroups ofLarentiinae are poorly known. In this study we present the most comprehensive attempt to date to resolve the phylogeny ofLarentiinae, having sampled at least one species from all currently recognized 23 tribes. Fragments of one mitochondrial (COI) and eight nuclear (EF‐1α,WGL,GAPDH,RPS5,IDH,MDH,CADand28S) genes were sequenced, for a total of 6939 bp. Maximum likelihood andBayesian analyses resulted in identical well‐resolved phylogenetic trees, which had maximum or near‐maximum support values at most nodes. Almost all conventionally recognized tribes represented by more than one genus were found to be monophyletic. Close to the root ofLarentiinae, six tribes branch off the main lineage one after another, withDyspteridini being sister to all other members of the subfamily. The rest of larentiines are divided into two very diverse lineages, comprising eight and at least ten tribes, respectively. There were just three findings incongruent with the conventional tribal subdivision of the subfamily. First, the generaCollixGuenée andAnticollixProut formed a separate, previously unrecognized but well‐supported clade at the tribe level. Second, thePalaearctic genusPelurgaHübner was placed apart fromLarentiaTreitschke andMesoleucaHübner, which were the other members ofLarentiini in this analysis. Third,Cataclysmini appeared together with genera belonging toXanthorhoini, leaving the latter paraphyletic. TheNeotropic genusOligopleuraHerrich‐Schäffer is shown to belong to the tribeEuphyiini (comb.n.) according to both molecular data and male genital morphology. The results and the tribal classification ofLarentiinae are discussed with reference to the principal publications since the end of the 19thCentury. We conclude that the current tribal classification ofLarentiinae is not controversial from the phylogenetic point of view and that its increasing complexity has merely reflected the accumulation of information, mainly through different methods of biosystematic study having become available for researchers. Our results indicate that diurnal lifestyle, accompanied by conspicuous coloration, has evolved independently in several subgroups ofLarentiinae.

Advances in molecular systematics of the vetigastropod superfamily Trochoidea

Williams, S.T. (2012). Advances in molecular systematics of the vetigastropod superfamily Trochoidea. —Zoologica Scripta, 41, 571–595.The gastropod superfamily Trochoidea Rafinesque, 1815 is comprised of a diverse range of species, including large and charismatic species of commercial value as well as many small or enigmatic taxa that are only recently being represented in molecular studies. This study includes the first sequences for rarely collected species from the genera Gaza Watson, 1879, Callogaza Dall, 1881, Antimargarita Powell, 1951 and Kaiparathina Laws, 1941. There is also greater taxon sampling of genera that have proved difficult to place in previous phylogenetic analyses, like Tectus Montfort, 1810, Tegula Lesson, 1832, Margarites Gray, 1847, Margarella Thiele, 1893 and trochoid skeneimorphs. There is also greater sampling of poorly represented families Solariellidae and Liotiidae. Bayesian analysis of combined gene data sets based on four (28S, 12S, 16S and COI) or five genes (plus 18S) suggests that there are eight, possibly nine families in Trochoidea including the families Margaritidae and Tegulidae, which are recognized for the first time at familial rank. Other trochoidean families confirmed are Calliostomatidae, Liotiidae, Skeneidae, Solariellidae, Trochidae and Turbinidae. A clade including Cittarium and the commercially important genera Rochia and Tectus may represent a possible ninth family, but this is not formally recognized or described here and awaits confirmation from further studies. Relationships among families were not generally well supported except in the 5‐gene tree. In the 5‐gene tree, Turbinidae, Liotiidae, Tegulidae, Cittarium, Rochia and Tectus form a well‐supported clade consistent with the previous molecular and morphological studies linking these groups. This clade forms another well‐supported clade with Margaritidae and Solariellidae. Trochidae is sister to Calliostomatidae with strong support. Subfamilial relationships within Trochidae are consistent with recent molecular studies, with the addition of one new subfamily, Kaiparathininae Marshall 1993 (previously a tribe). Only two subfamilies are recognized within Turbinidae, both with calcareous opercula: Prisogasterinae and Turbininae. Calliostomatidae includes a new subfamily Margarellinae. Its assignment to Calliostomatidae, although well supported by molecular evidence, is surprising considering morphological evidence.

Phylogenetic relationships in the subfamily Psychodinae (Diptera, Psychodidae)

Espíndola, A., Buerki, S., Jacquier, A., Ježek, J. & Alvarez, N. (2012). Phylogenetic relationships in the subfamily Psychodinae (Diptera, Psychodidae). —Zoologica Scripta, 41, 489–498.Thanks to recent advances in molecular systematics, our knowledge of phylogenetic relationships within the order Diptera has dramatically improved. However, relationships at lower taxonomic levels remain poorly investigated in several neglected groups, such as the highly diversified moth‐fly subfamily Psychodinae (Lower Diptera), which occurs in numerous terrestrial ecosystems. In this study, we aimed to understand the phylogenetic relationships among 52 Palearctic taxa from all currently known Palearctic tribes and subtribes of this subfamily, based on mitochondrial DNA. Our results demonstrate that in light of the classical systematics of Psychodinae, none of the tribes sensu Ježek or sensu Vaillant is monophyletic, whereas at least five of the 12 sampled genera were not monophyletic. The results presented in this study provide a valuable backbone for future work aiming at identifying morphological synapomorphies to propose a new tribal classification.

Bionomics, taxonomy, and distribution of the major malaria vector taxa of Anopheles subgenus Cellia in Southeast Asia: An updated review

There is high diversity of Anopheles mosquitoes in Southeast Asia and the main vectors of malaria belong to complexes or groups of species that are difficult or impossible to distinguish due to overlapping morphological characteristics. Recent advances in molecular systematics have provided simple and reliable methods for unambiguous species identification. This review summarizes the latest information on the seven taxonomic groups that include principal malaria vectors in Southeast Asia, i.e. the Minimus, Fluviatilis, Culicifacies, Dirus, Leucosphyrus, and Sundaicus Complexes, and the Maculatus Group. Main issues still to be resolved are highlighted. The growing knowledge on malaria vectors in Southeast Asia has implications for vector control programs, the success of which is highly dependant on precise information about the biology and behavior of the vector species. Acquisition of this information, and consequently the application of appropriate, sustainable control measures, depends on our ability to accurately identify the specific vectors.

Revised minimal standards for description of new species of the class Mollicutes (division Tenericutes)

Minimal standards for novel species of the class Mollicutes (trivial term, mollicutes), last published in 1995, require revision. The International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Mollicutes proposes herein revised standards that reflect recent advances in molecular systematics and the species concept for prokaryotes. The mandatory requirements are: (i) deposition of the type strain into two recognized culture collections, preferably located in different countries; (ii) deposition of the 16S rRNA gene sequence into a public database, and a phylogenetic analysis of the relationships among the 16S rRNA gene sequences of the novel species and its neighbours; (iii) deposition of antiserum against the type strain into a recognized collection; (iv) demonstration, by using the combination of 16S rRNA gene sequence analyses, serological analyses and supplementary phenotypic data, that the type strain differs significantly from all previously named species; and (v) assignment to an order, a family and a genus in the class, with an appropriate specific epithet. The 16S rRNA gene sequence provides the primary basis for assignment to hierarchical rank, and may also constitute evidence of species novelty, but serological and supplementary phenotypic data must be presented to substantiate this. Serological methods have been documented to be congruent with DNA-DNA hybridization data and with 16S rRNA gene placements. The novel species must be tested serologically to the greatest extent that the investigators deem feasible against all neighbouring species whose 16S rRNA gene sequences show >0.94 similarity. The investigator is responsible for justifying which characters are most meaningful for assignment to the part of the mollicute phylogenetic tree in which a novel species is located, and for providing the means by which novel species can be identified by other investigators. The publication of the description should appear in a journal having wide circulation. If the journal is not the International Journal of Systematic and Evolutionary Microbiology, copies of the publication must be submitted to that journal so that the name may be considered for inclusion in a Validation List as required by the International Code of Bacteriological Nomenclature (the Bacteriological Code). Updated informal descriptions of the class Mollicutes and some of its constituent higher taxa are available as supplementary material in IJSEM Online.

Major evolutionary events in the origin and diversification of the fern genus Polystichum (Dryopteridaceae)

Recent advances in molecular systematics of the ferns make it possible to address long-standing questions about classification of the major fern genera, such as the worldwide genus Polystichum (Dryopteridaceae), comprising at least 200 species. In this study we examined rbcL sequences and morphological characters from 55 fern taxa: 34 were from Polystichum and 21 were from other genera in the Dryopteridaceae. We found that Phanerophlebia, possibly including Polystichopsis, is the sister group to Polystichum sensu lato (s.l.), including Cyrtomium. Polystichum as commonly recognized is paraphyletic. Our results lead us to suggest recognizing the clade of earliest diverging Polystichum species as a distinct genus (Cyrtomidictyum) and to continue to recognize Cyrtomium as a separate genus, leaving a monophyletic Polystichum sensu stricto (s.s.). We resolved a tropical American clade and an African clade within Polystichum s.s. However, the resemblance between the once-pinnate, bulb-bearing calciphilic species found in Asia and the West Indies appears to be the result of convergent evolution. Optimizing our morphological character transformations onto the combined phylogeny suggests that the common ancestor of Polystichum s.l. and Phanerophlebia had evolved the common features of the alliance, including ciliate petiole-base scales, once-pinnate fronds, ultimate segments with scarious tips, peltate indusia, and microscales.

Lice and cospeciation: A response to barker

“The student who intends working on the Mallophaga should take warning that he will be tried almost beyond endurance by the paradoxes and complexities which beset his subject but he will also find, in the dual and inter-related aspect of insect and bird, an infinite fascination.” (Rothschild & Clay, 1952: pp. 156–157). The study of host-louse coevolution will benefit greatly from the phylogenetic perspective offered by recent advances in molecular systematics. However, in order to make best use of phylogenies we need to appreciate the complexities of the possible relations between host and parasite phylogeny. At the same time, the very complexity of louse-host systems has a potentially useful consequence; the presence of multiple lineages of lice on the same hosts allow for replicated tests of coevolutionary hypotheses. For example, if a number of louse clades infest the same host clade but some lice show more cospeciation than others, we might ask whether there are features of louse biology that correlate with this difference in host tracking fidelity. It may further be possible to ascertain the relative importance of these features in ccological time through controlled transfer experiments. By beginning to appreciate “the paradoxes and complexities” of host-louse evolution, lice may offer us not only “infinite fascination” but also a chance to address important questions in coevolution.