Complete phylogeny of Micrathena spiders suggests multiple dispersal events among Neotropical rainforests, islands and landmasses, and indicates that Andean orogeny promotes speciation

The Neotropical region is the most diverse on the planet, largely owing to its mosaic of tropical rainforests. Multiple tectonic and climatic processes have been hypothesized to contribute to generating this diversity, including Andean orogeny, the closure of the Isthmus of Panama, the GAARlandia land bridge and historical connections among currently isolated forests. Micrathena spiders are diverse and widespread in the region, and thus a complete phylogeny of this genus allows the testing of hypotheses at multiple scales. We estimated a complete, dated phylogeny using morphological data for 117 Micrathena species and molecular data of up to five genes for a subset of 79 species. Employing event-based approaches and biogeographic stochastic mapping while considering phylogenetic uncertainty, we estimated ancestral distributions, the timing and direction of dispersal events and diversification rates among areas. The phylogeny is generally robust, with uncertainty in the position of some of the species lacking sequences. Micrathena started diversifying around 25 Ma. Andean cloud forests show the highest in-situ speciation, while the Amazon is the major dispersal source for adjacent areas. The Dry Diagonal generated few species and is a sink of diversity. Species exchange between Central and South America involved approximately 23 dispersal events and started ~20 Ma, which is consistent with a Miocene age for the Isthmus of Panama closure. We inferred four dispersal events from Central America to the Antilles in the last 20 Myr, indicating the spiders did not reach the islands through the GAARlandia land bridge. We identified important species exchange routes among the Amazon, Andean cloud forests and Atlantic forests during the Plio-Pleistocene. Sampling all species of the genus was fundamental to the conclusions above, especially in identifying the Andean forests as the area that generated the majority of species. This highlights the importance of complete taxonomic sampling in biogeographic studies.

Morphological and molecular data in the study of the evolution, population genetics and taxonomy of Rhizostomeae

Rhizostomeae research based on morphological approaches was reinforced and diversified by new techniques after the 1970s, including developing methodologies for phylogenetic analysis, the rise of the polymerase chain reaction, and the emergence of different sequencing technologies. Here, we summarize the contribution of morphological and molecular data to the study of the classification and phylogenetic relationships of Rhizostomeae in addition to the use of molecular data in studies at the population, species, and supraspecific levels. Throughout the history of the study of the Rhizostomeae systematics, morphological data have been neglected when it comes to phylogenetic inferences, which is reflected in the lack of a phylogenetic analysis of the taxa within Rhizostomeae based on phenotypic characters of the adult medusa. Concerning molecular data, ca. 3,200 nucleotide sequences are available in GenBank and are mainly used for discovering, delimiting, describing, and identifying species. Molecular approaches have also allowed species monitoring by qPCR and metabarcoding of environmental DNA, as well as unveiling the distribution and genetic diversity of jellyfish populations, shedding light on introduction events, conservation, and health of edible jellyfish stocks. Nucleotide sequences have also been key for the development of phylogenetic hypotheses that serve as basis for investigations on the origin and diversification of morphological, ecological, and behavioral traits within Cnidaria; however, despite the progress achieved, phylogenetic uncertainty still exists, especially within the formerly known superfamily Inscapulatae. Future directions in Rhizostomeae research involve generating molecular and morphological data of neglected taxa, which represents a golden opportunity to understand the evolution of Rhizostomeae.

Phylogenetic relationships of the Geoplaninae land planarians (Platyhelminthes, Tricladida) assessed with a total evidence approach, with the description of a new species of Gigantea

Several studies have focused on the phylogenetic relationships within the Geoplaninae land planarians (Tricladida). In those studies, ancient phylogenetic relationships remained obscure. In this work, the phylogeny of Geoplaninae is assessed through three different datasets, namely morphological, molecular, and both datasets combined, i.e, a total evidence approach (TE). The data matrix consisted of six DNA regions, including a newly developed marker (DOM5), and a morphological matrix with 37 characters. The study produced the best-resolved hypothesis so far for the phylogeny of Geoplaninae, although ancient clades still remain elusive. The effect of the morphological data on the TE tree topology and clade support is seemingly negligible. The phylogenetic tree also suggests that most of the diagnostic morphological characters of the genera are homoplastic, while unambiguous unique synapomorphies can characterize some supra-generic informal groupings.

Revision and phylogenetics of the Neotropical sheet weaving spider genus

The Mounded Posterior Median Eyes (MPME) clade is a group of linyphiid spiders characterized by having posterior median eyes (PME) on a mound. The species diversity of this lineage, especially in the Neotropical region, is still largely unknown. In this study, we tackled one of the MPME groups, the genus Diplothyron Millidge, 1991. We have studied numerous specimens from both museums and freshly collected specimens to monograph Diplothyron. We also compiled both morphological and behavioral data from Diplothyron and representatives of higher-level lineages within Linyphiidae and several potential MPME groups to infer the phylogenetic relationships. We redescribed the type species, Diplothyron fuscus Millidge, 1991 and described the previously unknown male, and six new species: Diplothyron ballesterosi sp. nov., D. dianae sp. nov., D. monteverde sp. nov., D. nubilosus sp. nov., D. sandrae sp. nov. and D. solitarius sp. nov. We also transferred the following species from Linyphia to Diplothyron based on the study of the type material: D. chiapasia (Gertsch & Davies, 1946) comb. nov., D. linguatulus (F.O. Pickard-Cambridge, 1902) comb. nov., D. nigritus (F.O. Pickard-Cambridge, 1902) comb. nov., D. simplicatus (F.O. Pickard-Cambridge, 1902) comb. nov. and D. trifalcatus (F.O. Pickard-Cambridge, 1902) comb. nov. Diplothyron species are mainly found in the cloud forests of Central and South America, with the distribution stretching from the Colombian Andes to the Mexican Sierra Madre across the Central American mountain chains. We also provide a detailed morphological comparison between Diplothyron and closely related genera in the MPME clade, focusing on the genital morphology, including identification keys to both the MPME genera and species of Diplothyron. Our cladistic analyses recovered Diplothyron as a monophyletic group placed within the MPME clade. A newly circumscribed lineage now includes the genera Diplothyron, Dubiaranea Mello-Leitão, 1943; Linyphia Latreille, 1804; Lomaita Bryant, 1948; Microlinyphia Gerhardt, 1928; Neriene Blackwall, 1833; Notiohyphantes Millidge, 1985; Novafrontina Millidge, 1991 and Pityohyphantes Simon, 1929.

An integrative approach reveals high species diversity in the primitively segmented spider genus

Accurate species delimitation is crucial for our understanding of evolution, biodiversity and conservation. However, morphology-based species delimitation alone appears to be prone to taxonomic errors and ineffective for taxa with high interspecific morphological homogeneity or intraspecific morphological variations, as is the case for mesothele and mygalomorph spiders. Combined molecular–morphology species delimitation has shown great potential to delimit species boundaries in such ancient lineages. In the present study, molecular and morphological evidence were integrated to delimit species of the primitively segmented spider genus Songthela Ono, 2000. The cytochrome c oxidase subunit I gene (COI) was sequenced for 192 novel specimens belonging to 12 putative morphospecies. The evolutionary relationships within Songthela and the 12-morphospecies hypothesis were tested in two steps – species discovery and species validation – using four single-locus species delimitation approaches. All species delimitation analyses supported the 12-species hypothesis. Phylogenetic analyses yielded three major clades in Songthela, which are consistent with morphology. Accordingly, we assigned 19 known and 11 new species (S. aokoulong, sp. nov., S. bispina, sp. nov., S. dapo, sp. nov., S. huayanxi, sp. nov., S. lianhe, sp. nov., S. lingshang, sp. nov., S. multidentata, sp. nov., S. tianmen, sp. nov., S. unispina, sp. nov., S. xiujian, sp. nov., S. zizhu, sp. nov.) of Songthela to three species-groups: the bispina-group, the multidentata-group and the unispina-group. Another new species, S. zimugang, sp. nov., is not included in any species groups, but forms a sister lineage to the bispina- and unispina-groups. These results elucidate a high species diversity of Songthela in a small area and demonstrate that integrating morphology with COI-based species delimitation is fast and cost-effective in delimiting species boundaries. http://zoobank.org/urn:lsid:zoobank.org:pub:AF0F5B31-AFAF-4861-9844-445AE8678B67

Total evidence and sensitivity phylogenetic analyses of egg-brooding frogs (Anura: Hemiphractidae)

We study the phylogenetic relationships of egg-brooding frogs, a group of 118 neotropical species, unique among anurans by having embryos with large bell-shaped gills and females carrying their eggs on the dorsum, exposed or inside a pouch. We assembled a total evidence dataset of published and newly generated data containing 51 phenotypic characters and DNA sequences of 20 loci for 143 hemiphractids and 127 outgroup terminals. We performed six analytical strategies combining different optimality criteria (parsimony and maximum likelihood), alignment methods (tree- and similarity-alignment), and three different indel coding schemes (fifth character state, unknown nucleotide, and presence/absence characters matrix). Furthermore, we analyzed a subset of the total evidence dataset to evaluate the impact of phenotypic characters on hemiphractid phylogenetic relationships. Our main results include: (i) monophyly of Hemiphractidae and its six genera for all our analyses, novel relationships among hemiphractid genera, and non-monophyly of Hemiphractinae according to our preferred phylogenetic hypothesis; (ii) non-monophyly of current supraspecific taxonomies of Gastrotheca, an updated taxonomy is provided; (iii) previous differences among studies were mainly caused by differences in analytical factors, not by differences in character/taxon sampling; (iv) optimality criteria, alignment method, and indel coding caused differences among optimal topologies, in that order of degree; (v) in most cases, parsimony analyses are more sensitive to the addition of phenotypic data than maximum likelihood analyses; (vi) adding phenotypic data resulted in an increase of shared clades for most analyses.

Systematics of the Neotropical spider genera Jalapyphantes and Selenyphantes and the circumscription of the Pocobletus clade (Araneae: Linyphiidae)

We have revised the linyphiid genera Jalapyphantes and Selenyphantes. Jalapyphantes now includes five species, one of them new (J. tricolor sp. nov.). Selenyphantes now consists of six species of which five are new (S. costaricensis sp. nov., S. gaimani sp. nov., S. iztactepetl sp. nov., S. orizabae sp. nov. and S. volcanicus sp. nov.). To infer the phylogenetic position of Jalapyphantes and Selenyphantes, we analysed nucleotide sequence data from five markers (16S,18S, 28S, COI and histone H3) combined with morphological and behavioural data. Both genera are monophyletic and sister to each other. Both Jalapyphantes and Selenyphantes are included within the newly circumscribed Pocobletus clade, which includes all known species of Pocobletus plus several undescribed species. Pocobletus has nomenclatural priority over the junior synonyms Exechopsis, Exocora and Graphomoa.

Ocrepeira klamt sp. n. (Araneae: Araneidae), a novel spider species from an Andean páramo in Colombia

Herein we describe Ocrepeira klamt sp. n. (Araneae: Araneidae), a new orb-weaving spider species from a Colombian páramo, which was formerly inaccessible for scientific studies due to decades long armed conflicts. Both, phenotypic and molecular data are used to confirm genus affiliation, and the new species is placed into phylogenetic context with other araneid spiders. Morphological characteristics and ecological notes of Ocrepeira klamt sp. n. are reported together with the sequence of the barcoding region of cytochrome c oxidase subunit I (COI) to provide a comprehensive description of the spider, facilitating future identification beyond taxonomic experts. With this study we contribute to the taxonomic knowledge that is required to inventory the hyper diverse yet threatened ecosystem of the Colombian páramos.

Phylogenetic placement of the stone-nest orb-weaving spider Nemoscolus Simon, 1895 (Araneae : Araneidae) and the description of the first species from Australia

The spider genus Nemoscolus Simon, 1895 (Araneidae) has been neglected taxonomically despite the unique retreat that several species construct in their horizontal orb-webs, composed of pebbles and other detritus. The distribution of Nemoscolus is poorly known and the genus includes species from Africa and Europe. Nemoscolus is placed in Simon’s Cycloseae species group along with Cyclosa Menge, 1866, Acusilas Simon, 1895, Arachnura Vinson, 1863, Witica O. Pickard-Cambridge, 1895, among others. Here we describe a new species from Queensland, Australia, N. sandersi, sp. nov., drastically expanding the distribution range of the genus. We use nucleotide sequence data to phylogenetically place Nemoscolus using model-based inference methods within Araneidae and to explore its affinities to Simon’s Cycloseae. The data support propinquity of Nemoscolus with Acusilas and Arachnura but not with Cyclosa. Our analyses suggest that Cycloseae is not a clade, with Cyclosa, Acusilas, Witica and Nemoscolus not sharing a recent common ancestor. This use of an integrated granular retreat represents at least the second independent evolution of such a structure within Araneidae. These results improve our understanding of both phylogeny and retreat evolution in araneid spiders.