Nucleotide sequence variation in the ITS1-5.8S-ITS2 region of nuclear ribosomal DNA (nrDNA) from 70 populations of Mielichhoferia elongata and M. mielichhoferiana, plus two outgroup species, was analysed using maximum parsimony and maximum likelihood methods. High levels of nucleotide substitution and numerous insertion-deletion events were detected within and between the two species. M. elongata is monophyletic with regard to nrDNA variation, but M. mielichhoferiana is paraphyletic. (M. elongata is nested within it.) A clade within M. mielichhoferiana provides evidence of vicariance, with North American and Scandinavian sister groups of populations. Two major clades are resolved in M. elongata by sequence data that are completely congruent with previous isozyme work. One clade includes populations from both North America and Europe whereas the other is strictly North American. These two clades, resolved by multiple independent loci, clearly represent cryptic species within the morphologically uniform M. elongata. Certain geographical areas, most notably southwestern Colorado in Ouray and San Juan Counties, harbour diverse populations of M. elongata with distinct phylogenetic and phylogeographical histories. Morphologically indistinguishable but phylogenetically distant populations were detected a few metres apart at one site. In contrast, all populations collected over hundreds of kilometres in California belong to a single clade. Arctic North American populations belong to a clade that includes disjunct populations in Alaska, northern Ellesmere Island, and the northeastern USA, but not subarctic Swedish populations, which are more closely related to plants from the Rocky Mountains. Morphological uniformity belies complex infraspecific phylogenetic patterns within M. elongata and M. mielichhoferiana.

Molecular phylogeography and cryptic speciation in the mosses, Mielichhoferia elongata and M. mielichhoferiana (Bryaceae).

Detailed analysis of 270 specimens of Conocephalum conicum (L.) Dumort., mainly from the POZW Herbarium revealed some diagnostic differences between two cryptic species originally detected on the basis of isozyme studies. Several diagnostic characters were found in the structure of the archegoniophore, sporophyte and sterile thallus. The most reliable diagnostic features are size and structure of stomatal apparatus of the archegoniophore ‘heads’, type of junction of the air chamber walls with epidermal cells, and the thallus surface details. On the basis of morphological and anatomical diagnostic characters, two formerly cryptic species are recognized following the rules of formal taxonomy. The lectotype of C. conicum preserved in FI was found to possess characteristics of cryptic species C. conicum- species L. Accordingly, the species previously named as C. conicum–species L must bear the name Conocephalum conicum (L.) Dumort. No published name was related to C. conicum – species S, which is therefore described as a new species: Conocephalum salebrosum Szweykowski, Buczkowska & Odrzykoski. Both species are fully described and their diagnostic characters are illustrated. Distribution maps for both species are given.

Conocephalum salebrosum (Marchantiopsida, Conocephalaceae) – a new Holarctic liverwort species

Maximum likelihood and parsimony analyses of nrITS1-5.8S-ITS2 sequences place Austrian Herbertus sendtneri in a well boot- strap supported clade with Herbertus azoricus and Neotropical accessions which were alter- natively assigned to Herbertus subdentatus or Herbertus dicranus. Asian and African Herber- tus dicranus form a separate lineage which is placed sister to several European Herbertus taxa. Herbertus borealis from the British Isles is placed sister to H. stramineus in a robust sister relationship, indicating that the species does not belong in the synonymy of H. dicranus. As a result of the molecular investigation, the range of Herbertus sendtneri is extended to the Neotropics and H. azoricus is placed into the synonymy of H. sendtneri. Without much doubt, Herbertus dicranus does not occur in tropical America. Morphologi- cally, H. sendtneri and H. dicranus can at most be separated by weak tendencies. Herbertus sendtneri is characterized by the frequent occurrence of coarse appendages at the leaf margins and often completely papillose leaves. H. dicranus often has small appendages and a nearly smooth basal leaf half. Herbertus borealis, which is nonmonophyletic with H. dicranus in the molecular trees, cannot be separated morphologically from forms of H. dicranus with small appendages. Herbertus subdentatus is not identical with H. sendtneri. Morphological homoplasy and cryptic specia- tion are obviously common in Herbertus.

Cryptic speciation in Herbertus (Herbertaceae, Jungermanniopsida): Range and morphology of Herbertus sendtneri inferred from nrITS sequences

 Premise of the study : Recognition and formalization of morphologically cryptic species is a major challenge to modern taxonomy. An extreme example in this regard is the Holarctic Porella platyphylla s.l. ( P. platyphylla plus P. platyphylloidea ). Earlier studies demonstrated the presence of three isozyme groups and two molecular lineages. The present investigation was carried out to elucidate the molecular diversity of P. platyphylla s.l. and the distribution of its main clades, and to evaluate evidence for the presence of one vs. several species.  Methods : We obtained chloroplast ( atp B- rbc L, trn L- trn F) and nuclear ribosomal (ITS) DNA sequences from 101 Porella accessions ( P. platyphylla s.l., P. × baueri , P. cordaeana , P. bolanderi , plus outgroup species) to estimate the phylogeny using parsimony and likelihood analyses. To facilitate the adoption of Linnean nomenclature for molecular lineages, we chose a DNA voucher as epitype.  Key results : Phylogenies derived from chloroplast vs. nuclear data were congruent except for P. platyphylla s.l., including a North American lineage that was placed sister to P. cordaeana in the chloroplast DNA phylogeny but sister to the Holarctic P. platyphylla s.str. in the nuclear DNA phylogeny. European and North American accessions of P. cordaeana and P. platyphylla form sister clades.  Conclusions : The genetic structure of P. platyphylla s.l. refl ects morphologically cryptic or near cryptic speciation into Holarctic P. platyphylla s.str. and North American P. platyphylloidea . The latter species is possibly an ancient hybrid resulting from crossings of P. cordaeana and P. platyphylla s.str. and comprises several distinct molecular entities.

https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.3732/ajb.1100115

Formalizing morphologically cryptic biological entities: New insights from DNA taxonomy, hybridization, and biogeography in the leafy liverwort Porella platyphylla (Jungermanniopsida, Porellales)

A phylogeny of Porella (Porellaceae, Jungermanniopsida) based on nuclear and chloroplast DNA sequences.

Morphological and genetic variation in porella platyphylla and p. platyphylloidea and their systematic implications

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Morphological and genetic variation in porella platyphylla and p. platyphylloidea and their systematic implications