Morphological Species Concept Research Articles

An integrative approach to the delineation of locally endemic species: A case study of Vitis baihuashanensis (Vitaceae) and its implication for conservation management

Species definition and classification have long been the subject of controversy, and name changes can often be a source of frustration for both conservationists and the public. Vitis baihuashanensis is a critically endangered grapevine endemic to Beijing with only two remaining wild individuals. Although formerly treated as a synonym of V. amurensis, it was later listed in the List of National Key Protected Wild Plants (LNKPWP) in 2021. Here, we evaluated the taxonomic identity of V. baihuashanensis based on phylogenomic inference and population genetic analysis, and tested the species boundaries under various major species concepts (biological, morphological, ecological, phylogenetic, and integrative species concepts). Phylogenetic inference revealed that the amurensis-baihuashanensis clade was monophyletic, samples of V. baihuashanensis nested within the V. amurensis node. Population genetic analysis demonstrated that V. baihuashanensis samples clustered with V. amurensis. Our findings from field observations, morphological comparisons, pollination experiments, and genetic analyses indicate that V. baihuashanensis and V. amurensis are the same species under the integrative species concept, and support the synonymy of V. baihuashanensis under V. amurensis. Given that V. baihuashanensis was listed in the LNKPWP, we suggest that it be removed in the next update of the list because of limited financial resources. Nevertheless, the two wild individuals deserve conservation attention because of their distinct leaf characteristics and potential of cold tolerance, which could have important applications in the horticulture and grape industries. Our study provides multiple lines of evidence for clarifying the identity of a taxonomically questionable species, as well as valuable suggestion with conservation and management implications.

Species and Speciation in the Termite-Cultivated Fungus Termitomyces

Termitomyces is a genus of basidiomycete fungi cultivated by termites of the subfamily Macrotermitinae. This symbiosis originated in central Africa, and subsequently, the fungus-growing termites have colonized almost the entire African continent including Madagascar as well as significant parts of Asia. Around 40 species of Termitomyces have been described based on morphology of the sexual fruit bodies, which are associated with some 330 species of fungus-growing termites distributed over 11 genera. However, the total number of fungal species may be higher as not all species regularly produce mushrooms, and morphological variation does not seem to be a reliable criterion for species delimitation in this group. In this study we estimated the total number of species based on ITS-barcode criteria and assessed host specificity and geographic differentiation to infer patterns of speciation. We estimated the total number of phylogenetic species using two methods of DNA sequence-based species delimitation; Automatic Barcode Gap Discovery (ABGD) and the Generalized Mixed Yule Coalescent (GMYC) model on a large dataset of over 1,500 ITS sequences from laboratory cultures, fungarium specimens and the public database NCBI Genbank. This resulted in an estimated 87 species hypotheses using ABGD and 94 species hypotheses using the GMYC model. A phylogenetic reconstruction was performed on representative sequences of the 87 species hypotheses identified by ABGD (the most conservative estimate) constrained by a well-supported phylogeny based on whole-genome data to address host specificity and geographical differentiation. Five main clades were recovered which generally were associated with species of one or two host genera, except for samples collected from the genera Microtermes and Ancistrotermes, which formed two separate non-sister clades. We did not find any evidence for long-term host fidelity as would be expected for species with strict uniparental vertical symbiont transmission. We found strict geographic separation between African and Asian species of Termitomyces and infer a minimum of seven inter-continental migrations. We show that epigeous fruiting of the T. microcarpus group has a single evolutionary origin in Africa and that fruiting in species of this group likely is induced by the fungus rather than by the host-termite species. In contrast, fruiting in the symbionts of some species of Microtermes and Macrotermes may be suppressed by the host-termite species, since mushrooms of certain fungal species are found when those species are associated with some termite-host genera, but never when associated with other host genera. We discuss some examples of incongruence between morphological and phylogenetic species concepts and give suggestions to improve the taxonomy of the genus Termitomyces.

Phylogenetic analyses of the leafhopper tribe Chiasmini Distant, 1908 and delimination of species of the genus Exitianus Ball, 1929 (Hemiptera: Cicadellidae: Deltocephalinae: Chiasmini) in China based on molecular data

Previous phylogenetic analyses of the grass-specialist leafhopper tribe Chiasmini have resolved relationships among genera but have included few representatives of individual genera. Here the phylogeny of 20 Chinese species belonging to 8 chiasmine genera was investigated by combining DNA sequence data from two mitochondrial genes (COI, 16S) and two nuclear genes (H3, 28S). In both maximum likelihood (ML) and Bayesian inference (BI) analyses, relationships among genera were largely consistent with prior analyses, with most members of the tribe placed into two sister clades: (Exitianus + Nephotettix) and the remaining five sampled genera. To examine morphology-based species definitions in the taxonomically difficult genus Exitianus Ball, 1929, one mitochondrial gene (COI) and one nuclear gene (ITS2) were used to infer the phylogenetic relationships and status of two common and widespread species and compare the performance of different molecular species-delimitation methods. These analyses divide the included populations into two well-supported clades corresponding to current morphological species concepts but some inconsistencies occurred under the jMOTU, ABGD and bPTP methods depending on the which gene and analytical parameter values were selected. Considering the variable results yielded by methods employing single loci, the BPP method, which combines data from multiple loci, may be more reliable in Exitianus.

Fusarium species causing root rot and wilt in tomato in Brazil

AbstractA high frequency of plants showing symptoms of wilting and root rot has been observed in tomato‐producing areas in Santarém and Belterra, Pará, Brazil. These plants showed symptoms ranging from yellowing to wilting, with roots displaying reduced development and darkening of the xylem. Four fungal isolates, derived from a collection of 12 obtained from symptomatic plants, were chosen for identification using both morphological and phylogenetic species concepts. To determine the identity of the fungi, DNA was extracted and used in PCR reactions. PCR products were sequenced from the TEF‐1α and RBP2 regions and compared with sequences in GenBank using BLASTn. Based on the phylogenetic analyses, the isolates were identified as Fusarium falciforme and Fusarium suttonianum, belonging to the species complex Fusarium solani – (FSSC), and Fusarium triseptatum, belonging to the species complex Fusarium oxysporum – (FOSC). The fourth isolate, COUFPI 295, grouped within a clade of F. kalimantanense and F. sangayamense from FOSC. The fulfilment of Koch's postulates confirmed that all isolates induced symptoms of root rot and concomitant reduction in root mass, leading to observable wilting symptoms. This is the first report of F. suttonianum, F. falciforme and F. triseptatum causing root rot and wilt in tomato plants in Brazil.

Species delimitation in Amana (Liliaceae): transcriptomes battle with evolutionary complexity.

Species delimitation has long been a subject of controversy, and there are many alternative concepts and approaches used to define species in plants. The genus Amana (Liliaceae), known as "East Asian tulips" has a number of cryptic species and a huge genome size (1C = 21.48-57.35 pg). It also is intriguing how such a spring ephemeral genus thrives in subtropical areas. However, phylogenetic relationships and species delimitation within Amana are challenging. Here we included all species and 84 populations of Amana, which are collected throughout its distribution range. A variety of methods were used to clarify its species relationships based on a combination of morphological, ecological, genetic, evolutionary and phylogenetic species concepts. This evidence supports the recognition of at least 12 species in Amana. Moreover, we explored the complex evolutionary history within the genus and detected several historical hybridization and introgression events based on phylogenetic trees (transcriptomic and plastid), phylonetworks, admixture and ABBA-BABA analyses. Morphological traits have undergone parallel evolution in the genus. This spring ephemeral genus might have originated from a temperate region, yet finally thrives in subtropical areas, and three hypotheses about its adaptive evolution are proposed for future testing. In addition, we propose a new species, Amana polymorpha, from eastern Zhejiang Province, China. This research also demonstrates that molecular evidence at the genome level (such as transcriptomes) has greatly improved the accuracy and reasonability of species delimitation and taxon classification.

Still on the Stachytarpheta longispicata complex (Verbenaceae): two new narrowly endemic species from the Cerrado domain of Central Brazil

Among the Brazilian Stachytarpheta, the small group of species treated as the Stachytarpheta longispicata complex is morphologically recognised by its inflorescences with pedicellate flowers. This character is also present in S. longibracteata and S. rizzoi, two new species herein described based on the morphological species concept. Both species have a restricted distribution in the Cerrado domain, with S. longibracetata found in the Jalapão region (State of Tocantins) and S. rizzoi in the Serra Dourada region (State of Goiás). Detailed diagnosis, morphological comparisons, line drawings, ecological and taxonomic data, provisional conservation status, and a distribution map are provided for each new species. With these findings, we improve the taxonomy of the S. longispicata complex by increasing the number of known species to seven, and providing an identification key for this peculiar group with pedicellate flowers exclusive to the Cerrado.

Widespread coexistence of genetically distinct morphotypes in theSatyrium longicaudacomplex (Orchidaceae)

AbstractSpecies-level taxonomy is traditionally based on herbarium collections that typically include few, or even single, representatives per site. This can lead to underestimation of diversity when there are sympatric populations of superficially similar plants belonging to different lineages. Satyrium longicauda (Orchidaceae) represents a taxonomic challenge for the delimitation of species boundaries due to the high degree of morphological variation detected within and among populations. Currently, just two varieties are accepted based mainly on length differences of the lateral sepal and nectar spur. However, there is extensive morphological variation within South African populations and evidence for several pollination ecotypes, indicating that this taxon represents an actively diverging species complex. Here, we evaluate intraspecific morphological variation through uni- and multivariate morphometrics and analyse internal transcribed spacer sequences for individuals sampled from 36 sites, including 14 sites where divergent morphotypes occur sympatrically. Morphometric analyses of 1802 individuals revealed the presence of eight morphotypes based on vegetative and floral characters. Up to six morphologically and genetically distinct morphotypes can coexist in sympatry. Morphological and genetic distances among populations were significantly correlated. Phylogenetic analyses of 120 accessions indicated that neither of the two varieties nor S. longicauda as a species is monophyletic, and provided evidence for the monophyly of some of the morphotypes including the newly described S. cernuiflorum. The presence of distinct morphological and genetic sympatric variants, which in several cases scale up to distinct evolutionary lineages, is consistent with the existence of different taxa according to morphological and biological species concepts. Our results therefore confirm that taxonomy based mainly on herbarium collections can grossly under-estimate actual diversity of disparate lineages, although further work is required to finalize taxonomic decisions. These findings have implications for efforts to estimate species diversity in groups that are in the process of diversifying and for conservation practice.

The species problem in evolution education

An issue that might concern the species problem is the understanding and acceptance of evolution by students. The reason is that some of the modern concepts, which have been developed to define the species category, do not fit the evolutionary theory. In addition, some other concepts are simply criteria for the delimitation of species taxa. In particular, the biological and morphological species concepts, which are present in every textbook and are used almost exclusively in the teaching of evolution, can intensify students’ essentialist perceptions. However, these perceptions could be effectively dealt with the development of the species problem and the nature of species taxa in the classroom, and also the treatment of species as one more level of organization of biological systems during teaching process. This approach is employed in a lesson with a view to contributing to the structure of a fully developed conceptual framework by the students in order to understand the evolution.

Ancyronyx jhoanae sp. nov. (Coleoptera: Elmidae), A New Spider Riffle Beetle Species from Luzon, Philippines, and New Records for A. tamaraw Freitag, 2013

Ancyronyx jhoanae sp. nov., a new species of genus Ancyronyx Erichson, 1847 from Luzon is described using an integrative taxonomic approach. Illustrations of habitus and diagnostic characters are provided. Molecular analysis of a fragment of the COI 5’-end was employed to support the morphological species concept. Differences from closely related species based on molecular and morphological data are discussed. First records of A. tamaraw Freitag, 2013 from Luzon are reported.

A world generic revision of Quediini (Coleoptera, Staphylinidae, Staphylininae), part 1. Early diverging Nearctic lineages.

Several phylogenetically isolated, early diverging lineages of rove beetle tribe Quediini, all endemic to the western Nearctic, have recently been revealed by phylogenomic systematics. These three lineages, currently treated as either Quedius (Raphirus) or Q. (Paraquedius) warrant recognition at the genus level in the ongoing effort to achieve reciprocal monophyly of genera in Quediini. The three lineages were each morphologically studied in detail, with the following results: Paraquedius Casey, stat. res. is re-elevated to genus rank, Quediellus Casey, stat. res. is resurrected from synonymy and redefined, and Iratiquedius gen. nov. is described for the species of the Amabilis and Prostans groups. A morphological diagnosis is provided for each genus at both the global and regional (Nearctic) level. Species level revisions, with keys, are provided for Iratiquedius, Paraquedius, and Quediellus with the following results: Iratiquediusuncifer sp. nov. and Paraquediusmarginicollis sp. nov. are described, Quediellusnanulus Casey is treated as syn. nov. of Quediellusdebilis (Horn), and I.amabilis (Smetana), I.mutator (Smetana), and P.puncticeps (Horn) are substantially redefined. Where possible, CO1 barcode sequence data are integrated with the morphological species concepts used herein and their clusters were found to be congruent.

Exploring diatom diversity through cultures - a case study from the Bow River, Canada

Diatom cultures can help answer taxonomic, biogeographic and ecological questions on a local and global scale. Unialgal cultures are derived from a single cell and provide abundant material for morphological and molecular analyses. The link between the historic morphological species concept and the molecular data is becoming increasingly important with the use of eDNA metabarcoding. Additionally, cultures provide insights into the life cycle of diatoms and thereby complement taxonomy and species ecology. In this study, we present an approach to extract benthic diatoms from an environmental sample to generate unialgal cultures. We explored diatom diversity in preserved assemblages and by culturing as many different taxa as possible from benthic freshwater samples taken on the same day from the Bow River in Calgary, Canada. With both methods we found a total of 221 different benthic diatom taxa, of which 182 were identified in the preserved diatom assemblages. Interestingly, an additional 39 taxa only appeared in the cultures. In total 129 strains were cultivated representing 71 different taxa. This study includes pictures of living cells demonstrating the additional merits of unialgal cultures, as they provide information on plastid details, auxospores and endosymbionts. Both, the identification of the diatom assemblages and the generation and identification of strains provide the foundation for additional water quality assessment tools, taxonomic insights and molecular references libraries.

Three new species of Ancyronyx Erichson, 1847 (Coleoptera, Elmidae) from Mindanao, Philippines

Abstract Three new species of the genus Ancyronyx Erichson, 1847 from Greater Mindanao are described: A. kalasan sp. n., A. manobo sp. n., and A. zamboangaensis sp. n. Illustrations of habitus and line drawings of genitalia are presented. Molecular species delimitation using COI mtDNA barcodes supports the morphological species concept.

First molecular phylogeny and species delimitation of West PalaearcticPollenia(Diptera: Polleniidae)

AbstractCluster flies of the genus Pollenia are known as mass invaders of human dwellings, but are important plant pollinators in the temperate climatic zone. Despite being the most species-rich and widespread genus in Polleniidae, no study to date has tested infrageneric relationships using molecular data. Here we use three molecular markers, COI, Ef-1α and CAD to reconstruct the phylogenetic relationships between 18 West Palaearctic species of Pollenia, representing eight predefined morphological species groups, using both maximum likelihood and Bayesian approaches. We show several instances where morphological and molecular results are congruent, but also instances where they are discordant. We develop a COI barcode reference library for 18 species, containing newly generated data (87 sequences) and sequences retrieved from the Barcode of Life Data System (BOLD). We analyse this dataset using both Automatic Barcode Gap Discovery (ABGD) and Bayesian Phylogenetics & Phylogeography (BPP) methods to validate morphological species hypotheses and delimit species. The results of these species delimitation analyses were, in most cases, identical and aligned with predefined morphological species concepts. Based on the results of our analyses, we synonymize P. moravica (stat. rev.) with P. amentaria and assign 191 unidentified sequences from BOLD to named morphospecies.

Revision of the genus Pelecocera Meigen, 1822 (Diptera: Syrphidae) from France: taxonomy, ecology and distribution.

The occurrence and distribution of the various species of the genus Pelecocera Meigen, 1822 (Diptera: Syrphidae) occurring in France are revised and a new species, Pelecocera garrigae Lair Nve, 2022 sp. nov., is described from Mediterranean France. Distribution and ecological data of the six French species of Pelecocera are provided and an identification key is given to all these species. Sequences of the cytochrome c oxidase subunit I (COI) from all European Pelecocera species support the morphological species concept, except for Pelecocera scaevoides (Falln, 1817). The binomen Pelecocera lugubris Perris, 1839 is recovered to name the Pelecocera lusitanica (Mik, 1898) of authors in France.

Review of the Rheotanytarsus muscicola Species Group from China (Diptera: Chironomidae)

The Rheotanytarsus muscicola species group is generally considered to be a taxonomically difficult group of non-biting midges (Diptera: Chironomidae). In this study, we review the R. muscicola species group based on the adult males from China using morphology and DNA barcodes. Rheotanytarsus ferringtoni Lin & Yao sp. n. is described and figured, and four species (Rheotanytarsus falcipedius Kyerematen, Andersen & Sæther, 2000; Rheotanytarsus fluminis Kawai & Sasa, 1985; Rheotanytarsus illiesi Siebert, 1979; and Rheotanytarsus photophilus Goetghebuer, 1921) new to China are redescribed, figured and discussed. An updated key to known adult males of the R. muscicola species group is presented. Our study shows concordance between morphological species concepts and DNA barcodes.

How important was polyploidy in the diversification of herbs in the Chaquean Domain? The case of theTurnera sidoidesautopolyploid complex (Passifloraceae: Turneroideae)

AbstractThe evolutionary processes that shape the unique biodiversity of the Neotropical Chaquean Domain are still poorly understood, and choosing an appropriate model to address evolutionary questions is essential for understanding the current patterns of Chaquean diversity. We used the Turnera sidoides autopolyploid complex as a model to assess current and past environmental factors and the processes that shaped and maintain its intraspecific variation in the Chaquean Domain. Based on current and past niche modelling, cytogeographical and genetic divergence analyses, we provide strong evidence that the T. sidoides complex has been in an active process of intraspecific allopatric diversification at the diploid level since the early Pleistocene. Further diversification of the complex involved the emergence of independent polyploid series in each morphologically divergent lineage. Cytotypes in each series do not differ in diagnostic morphological traits, but are reproductively isolated and have different ecological requirements. Currently, each subspecies/morphotype and cytotype are true species according to the biological, evolutionary and ecological concepts; however, they are still considered to be the same morphological species. Our study has clarified the effect of the complex processes of diversification occurring in the Chaquean Domain on T. sidoides and that much diversity is overlooked when only the morphological species concept is considered when estimating the diversity of Neotropical ecoregions.

A morphometric analysis of the widespread Triplaris americana (Polygonaceae)1

Triplaris (Polygonaceae) is a genus of 18 species of fast-growing dioecious trees. Triplaris is widely distributed in the Neotropics, with a center of diversity in the western portion of the Amazon basin. The most recent revision of the genus was one of consolidation, lumping a large number of names into a small number of species concepts. One species in particular, T. americana, is presently an amalgamation of 15 historical taxonomic concepts. Moreover, as currently circumscribed, T. americana is morphologically variable and ranges over the whole of the Neotropics despite the fact that most species in the genus have restricted geographic ranges. Given the recent taxonomic history of Triplaris, the infraspecific variation observed in T. americana, and the narrow endemism observed in most species of Triplaris, it is reasonable to question whether T. americana, as it is currently circumscribed, in fact constitutes a single species. This study examined the circumscription of T. americana using a morphological species concept, morphometrics, and hierarchical clustering. Hierarchical clustering revealed that the morphological variation present in 136 specimens of T. americana could be explained by dividing those specimens into two groups of plants. These groups, however, could not be reliably distinguished morphologically. The distribution of values and morphologies among the various groups always overlapped. As a result, this work supports retaining T. americana as a single, widespread, and morphologically variable species.

Cryptic species and grey zone speciation of the Barbodes binotatus complex (Teleostei, Cyprinidae) in Sundaland.

Morphology-based taxonomy of freshwater fish is effective when there are representative specimens covering large regions. However, in Sundaland, where the presence of cryptic species is high, the technique has its limitations. This is compounded by uncritical descriptions of holotypes in old literature. We demonstrate the problem using Barbodes binotatus first described from an ink drawing. Several species in the Barbodes genus of Sundaland exhibit morphological similarity to B. binotatus. We applied new DNA sequences of 16S, cytochrome c oxidase subunit I (COI), cytochrome b (Cytb) and recombination-activating gene 1 (RAG1), and pigmentation markers to clarify species complex boundaries in the Malay Peninsula, namely B. aff. binotatus "Malay Peninsula", Barbodes cf. banksi and Barbodes rhombeus. Results suggest B. binotatus-like specimens in the Malay Peninsula are B. rhombeus based on a threshold of 3% COI genetic divergence. B. aff. binotatus recorded in Sumatra, Borneo and the Philippines are likely valid but undescribed species. However, if the 2% COI threshold is applied, some populations in the northern Malay Peninsula would qualify as new and undescribed species. The implications of the 2% threshold and the likelihood of "grey zone" incipient populations are discussed. We further found a rapid visual method, not reported previously, to delineate B. aff. binotatus and B. cf. banksi, but it requires further validation. Additionally, we offer fresh perspectives by discussing the roles of biological species concept, morphological species concept, genetic species concept and mate recognition concept in the B. binotatus complex. Our findings reinforce the standpoint that species delineation is not entirely a binary process, but there is a spectrum to consider, especially in biogeography intersection regions.

Three Oriental species of Pseudoaerumnosa Rudzinski (Diptera, Sciaridae) from China.

Three Oriental species of the genus Pseudoaerumnosa Rudzinski, 2006 from China are described and illustrated: P. regularis sp. n., P. tianmushana sp. n. and P. tkoci Vilkamaa, Halenius Ševčík, 2019. The morphological species concepts were supported by the DNA barcodes of COI sequences. The genetic distances of Pseudoaerumnosa species were analyzed and a neighbor-joining tree was constructed, based on 37 sequences of nine species.

Haploporus (Basidiomycota, Polyporales) in sub-Saharan Africa: Poria eichelbaumii, a long-forgotten name, is reinstated in Haploporus and H. grandisporus sp. nov. is proposed

Poria eichelbaumii, a long-forgotten name, is transferred to Haploporus based on studies of the type specimen, comparison with new collections, and evidences from both morphology and phylogeny. The species is redescribed and illustrated. Haploporus grandisporus is described as new, on the basis of concordant morphological and phylogenetic species concepts. These two species form two very closely related clades within the Haploporus lineage in [28S-ITS]-based phylogenetic inferences. Haploporus eichelbaumii and H. grandisporus are distinguished by the size of their basidiospores (11.5–14.5 × 5.0–6.0 μm, average = 12.7 × 5.8 μm, vs 14–17.5 × 6.0–7.3 μm, average 15.4 × 6.6 μm), the size of their pores (2.5–3.5 / mm, vs 1.5–2.5 / mm), and, likely, divergent autecologies. Although both species occur in montane ecosystems of the eastern African rift, the data so far available suggest they occupy different habitats. Haploporus eichelbaumii has wider distribution, spanning over both branches of the eastern rift, at elevation ~ 1500–2500 masl, in various vegetation types, mostly on small-sized dead branches or twigs, and dead bamboo culms. It is known so far from Kenya, Tanzania, and Malawi to the East, and western Burundi, western Uganda, and Eastern Congo (DRC) in the Albertine mountain ranges. Haploporus grandisporus is known, hitherto, only from the Eastern slopes of Mount Elgon in Kenya, at the timberline, 2900–3200 masl, mostly on dead heather branches (Erica arborea, Ericaceae) in heather thickets. Haploporus nanosporus is currently the third known Haploporus species from tropical Africa, known from the western edge of the Guineo-Congolian rain forest in Gabon and Cameroon. This species is also redescribed and illustrated.