Phylogenetic Relationships and Historical Biogeography of Cetopsorhamdia (Siluriformes: Heptapteridae), with Description of a New Species from the Orinoco Basin, Colombia

The Neotropics contain one of the most diverse assemblages of freshwater fishes worldwide. Part of this diversity is shared between the Orinoco and Amazon basins. These basins have been separated for a long time due to the Vaupes Arch, rising between 10-11 Ma. Today, there is only one permanent connection between the Orinoco and Negro (Amazon) basins, known as the Casiquiare Canal. However, alternative corridors allowing fish dispersion between both basins have been proposed. The cardinal tetra (Paracheirodon axelrodi), the most important fish in the ornamental world market, is distributed in both basins. Here we investigated P. axelrodi phylogeography, population structure, and potential routes of migration and connectivity between the two basins. A total of 468 bp of the mitochondrial gene (COI), 555 bp of the nuclear gene fragment (MYH6), and eight microsatellite loci were analyzed. As a result, we found two major genetic clusters as the most likely scenario (K=2), but they were not discreetly distributed between basins. A gradient of genetic admixture was observed in Cucui and São Gabriel da Cachoeira, between the upper Negro River and the upper Orinoco. Samples from the middle-lower Negro River were highly structured. Cucui (Negro basin) was more similar to the Orinoco than to the rest of the Negro basin populations. However, substructure was also observed by the discriminant analysis, fixation indices and other hierarchichal structure analyses (K=3-6), showing three major geographic clusters: Orinoco, Cucui, and the remaining Negro basin. Unidirectional migration patterns were detected between basins: via Cucui toward Orinoco and via the remaining of the Negro basin toward Orinoco. Results from the Relaxed Random Walk analysis support a very recent origin of this species in the headwater Orinoco basin (Western Guiana Shield, at late Pleistocene) with a later rapid colonization of the remaining Orinoco basin and almost simultaneously the Negro River via Cucui, between 0.115 until about 0.001 Ma. Historical biogeography and population genetic patterns observed here for Cardinal tetra, seem to be better explained by river capture, physical, or ecological barriers than due to the geographic distance.

A new species of Pristella is described from the Rio Meta drainage, Rio Orinoco basin, Colombia. Pristella ariporo, new species, is described as the second known species of the genus and differs from P. maxillaris by lacking maxillary teeth, possessing all teeth of premaxilla and dentary conical, by the absence of a dark blotch on the pelvic fin and the absence of a humeral blotch. The evaluation of the relationships of the new taxon within Characidae through an extensive phylogenetic analysis recovered Pristella as a monophyletic clade, sister to Bryconella pallidifrons. A new diagnosis of Pristella is provided. Hyphessobrycon axelrodi, the only species of this genus possessing only conical teeth, may actually be a species of Pristella.

Simple SummaryThis study focuses on New World Vultures, a group of seven scavenger bird species with ecological significance. Despite their importance, there is limited knowledge about their evolutionary history and conservation needs. Recent advances in understanding their evolutionary relationships have paved the way for addressing these gaps using phylogenetic methods. By analyzing the species’ ancestral distribution in the Americas, we employed two techniques to identify historical dispersion patterns. This study pinpointed South America as their original area, with subsequent recolonization of North America by certain species. To guide conservation efforts, we used two indices. The Evolutionary Distinctiveness (ED) index measured species’ uniqueness according to their phylogeny, while the Global Endangerment (GE) index mapped phylogenetic diversity. The findings highlighted the Black Vulture, California Condor and Andean Condor as priority species based on their uniqueness and evolutionary significance. Additionally, we identified crucial regions for conservation, including the lowlands of the Amazon River basin, the Orinoco basin and various areas along the Guiana Shield’s tributaries. This research underscores the importance of combining evolutionary and ecological insights and tools to fill knowledge gaps about species of concern. By doing so, we can formulate effective strategies to protect these species in the face of ongoing biodiversity loss.The New World Vultures (Cathartidae) include seven species of obligate scavengers that, despite their ecological relevance, present critical information gaps around their evolutionary history and conservation. Insights into their phylogenetic relationships in recent years has enabled the addressing of such information gaps through approaches based on phylogeny. We reconstructed the ancestral area in America of the current species using two regionalization schemes and methods: Biogeography with Bayesian Evolutionary Analysis (BioGeoBears) and Bayesian Binary Model–Monte Carlo Markov Chains (BBM–MCMC). Then, we identified the priority species and areas for conservation by means of the Evolutionary Distinctiveness index (ED), as a proxy of the uniqueness of species according to phylogeny, and the Global Endangerment index (GE), mapping phylogenetic diversity. We found that the ancestral area of New World Vultures in America corresponds to South America, with dispersal processes that led to a recolonization of North America by Coragyps atratus, Gymnogyps californianus and Cathartes aura. We identified the Black Vulture, G. californianus and Vultur gryphus as priority species based on ED and “Evolutionary Distinct Globally Endangered” (EDGE) indexes, and the lowlands of Amazon River basin and the Orinoco basin and some tributaries areas of the Guiana Shield were identified as the priority areas when mapping the phylogenetic diversity. This study highlights the importance of filling knowledge gaps of species of conservation concern through the integration of evolutionary and ecological information and tools and, thus, developing adequate strategies to enhance the preservation of these species in the face of the current loss of biodiversity.

BackgroundLittle is known about the diversity, phylogenetic relationships, and biogeography of trypanosomes infecting non-mammalian hosts. In this study, we investigated the influence of host species and biogeography on shaping the genetic diversity, phylogenetic relationship, and distribution of trypanosomes from South American alligatorids and African crocodilids.MethodsSmall Subunit rRNA (SSU rRNA) and glycosomal Glyceraldehyde Phosphate Dehydrogenase (gGAPDH) genes were employed for phylogenetic inferences. Trypanosomes from crocodilians were obtained by haemoculturing. Growth behaviour, morphology, and ultrastructural features complement the molecular description of two new species strongly supported by phylogenetic analyses.ResultsThe inferred phylogenies disclosed a strongly supported crocodilian-restricted clade comprising three subclades. The subclade T. grayi comprised the African Trypanosoma grayi from Crocodylus niloticus and tsetse flies. The subclade T. ralphi comprised alligatorid trypanosomes represented by Trypanosoma ralphi n. sp. from Melanosuchus niger, Caiman crocodilus and Caiman yacare from Brazilian river basins. T. grayi and T. ralphi were sister subclades. The basal subclade T. terena comprised alligatorid trypanosomes represented by Trypanosoma terena n. sp. from Ca. yacare sharing hosts and basins with the distantly genetic related T. ralphi. This subclade also included the trypanosome from Ca. crocodilus from the Orinoco basin in Venezuela and, unexpectedly, a trypanosome from the African crocodilian Osteolaemus tetraspis.ConclusionThe close relationship between South American and African trypanosomes is consistent with paleontological evidence of recent transoceanic dispersal of Crocodylus at the Miocene/Pliocene boundaries (4–5 mya), and host-switching of trypanosomes throughout the geological configuration of South American hydrographical basins shaping the evolutionary histories of the crocodilians and their trypanosomes.

BackgroundTo unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order.ResultsWe sequenced the genome of three Orestias species from the Andean Altiplano. Our analysis revealed that the small genome size in this genus (~ 0.7 Gb) was caused by a contraction in transposable element (TE) content, particularly in DNA elements and short interspersed nuclear elements (SINEs). Using predicted gene sequences, we generated a phylogenetic tree of Cyprinodontiformes using 902 orthologs extracted from all 32 available genomes as well as three outgroup species. We complemented this analysis with a phylogenetic reconstruction and time calibration considering 12 molecular markers (eight nuclear and four mitochondrial genes) and a stratified taxon sampling to consider 198 species of nearly all families and genera of this order. Overall, our results show that phylogenetic closeness is directly related to geographical distance. Importantly, we found that Orestias is not part of the Cyprinodontidae family, and that it is more closely related to the South American fish fauna, being the Fluviphylacidae the closest sister group.ConclusionsThe evolutionary history of the Orestias genus is linked to the South American ichthyofauna and it should no longer be considered a member of the Cyprinodontidae family. Instead, we submit that Orestias belongs to the Orestiidae family, as suggested by Freyhof et al. (2017), and that it is the sister group of the Fluviphylacidae family, distributed in the Amazonian and Orinoco basins. These two groups likely diverged during the Late Eocene concomitant with hydrogeological changes in the South American landscape.

This dataset contains the digitized treatments in Plazi based on the original journal article Vasudevan, Karthikeyan, Silva, Anslem De, Kar, Niladri Bhusan, Naniwadekar, Rohit, Lalremruata, Albert, Prasoona, Rebekah, Aggarwal, Ramesh K (2012): Phylogeography of Dasia Gray, 1830 (Reptilia: Scincidae), with the description of a new species from southern India. Zootaxa 3233: 37-51, DOI: 10.5281/zenodo.211627

A new species of the genus Kurixalus is described from the Central Highlands of Vietnam based on molecular phylogenetic and morphological analyses. Morphologically, Kurixalus motokawai sp. nov. is most similar to K. banaensis but they are clearly separated from each other in mitochondrial DNA sequences. In phylogenetic analysis the new species clustered in the same clade with Kurixalus banaensis and K. viridescens . However, the new species differs from K. banaensis by having a smaller body size, a higher ratio of forelimb length/SVL in both sexes, a smaller ratio of first toe length/SVL in males, snout tip less markedly pointed, and only weakly developed dermal appendages on the outer edges of fore- and hindlimbs. Kurixalus motokawai sp. nov. also differs from K. viridescens by having a smaller size in females and a brown dorsum with dark markings.

Red-headed Amazon River Turtles in Venezuela and Colombia: population separation and connection along the famous route of Alexander von Humboldt

The taxonomy of the genus Fredius Pretzmann, 1967, is reviewed, and new taxa are described: Fredius adpressus, F. adpressus piaroensis, F. platyacanthus, and F. estevisi siapensis. The 8 species of this genus inhabit 4 major basins of different geological age in northern South America. The Orinoco basin is the oldest, followed by the Essequibo-Cuyuni basin. The lower Amazon basin, formed from Tertiary to Holocene by alluvionic deposition, is younger than these two. The Atlantic area, formed mainly by marine regressions, is the youngest. The phylogenetic relationships within Fredius, studied by means of a cladistic analysis, were compared with the relationships of these areas using Brooks parsimony analysis. The phylogenetic data fully agree with the area cladogram. The position of the ancestors within the area cladogram shows that most of them were present in a hypothetical major basin comprising the present Orinoco, Essequibo, and Cuyuni rivers, and that much of the evolution of the group occurred there. There is some ambiguity about the possible origin of 2 widespread species. The most parsimonious explanation for one of them is that it originated in the Atlantic drainage and then dispersed into the lower Amazon basin.

The taxonomic revision of the genus Lamontichthys Miranda-Ribeiro, based on the examination of 164 specimens of different river drainages throughout the Amazon basin, revealed the presence of six species of which two are new. Lamontichthys filamentosus occurs in the upper and middle portions of the rio Amazonas basin; L. llanero in the río Orinoco basin; L. maracaibero in the lago Maracaibo basin; and L. stibaros in the upper río Amazonas basin. Lamontichthys avacanoeiro, new species, occurs in the upper rio Tocantins basin; and L. parakana, new species, in the lower rio Tocantins basin. The new species represent a considerable extension in the so far known distribution of the genus. A parsimony analysis, including 87 osteological and external morphological characters from Lamontichthys and related taxa (total of 16), resulted in three most parsimonious trees with 194 steps (CI = 0.73 and RI = 0.78). The hypothesis of monophyly of Lamontichthys is corroborated and supported by six derived characters. Within Lamontichthys two monophyletic assemblages are recognized, one includes L. avacanoeiro and L. stibaros, the other includes L. maracaibero and the clade formed by L. filamentosus and L. llanero. The relationships of Lamontichthys parakana, a species that was not included in the phylogenetic analysis is discussed. The monophyly and relationships of the monotypic genus Pterosturisoma microps are also discussed.

Pitheciids, one of the major radiations of New World monkeys endemic to South and Central America, are distributed in the Amazon and Orinoco basins, and include Callicebus, Cacajao, Chiropotes, and Pithecia. Molecular phylogenetics strongly support pitheciid monophyly, whereas morphological analyses infer a range of phylogenies including a sister relationship between Aotus and Callicebus. We collected geometric morphometric cranial data from pitheciids and Aotus, and used cranial data for distance-based phylogenetic analysis and tests of phylogenetic signal. Phylogenetic analyses of pitheciids were repeated with Lagothrix, Callimico, and Saimiri outgroups for Procrustes shape with and without Aotus based on the whole cranium and six anatomical regions. All phylogenetic signal tests were significant, and tree lengths were shortest and had the least morphological change over the phylogeny for Procrustes residuals from the cranial base and palate. The majority of phylogenetic analyses of Procrustes shape for pitheciids without Aotus supported the molecular phylogeny, and with Aotus included the majority inferred an Aotus-Callicebus clade, although three analyses with Callimico as outgroup supported the molecular phylogeny. The morphological similarity of Aotus and Callicebus is likely a mix of plesiomorphy, allometry, and homoplasy, and future phylogenetic inference of living and extinct platyrrhine taxa should consider the impact of these factors alongside outgroup selection and cranial region.

A new racer species, Coluber ( sensu lato ), is described from the small islands of Andeber, Nocra, and Sarad in the Dahlak archipelago. This polymorphous species is most closely related to C. ( s.l. ) florulentus (Geoffroy) and C. ( s.l. ) taylori Parker. Phylogenetic relationships and generic allocation of East African and Palaearctic racer genera are briefly discussed. Three species of amphibians are known from Dahlak al-Kabir, and a total of fifteen terrestrial reptile species including two endemic snakes, viz. the new species of Coluber ( s.l. ) and Echis megalocephalus , have been recorded from nine islands in the Dahlak archipelago.

A new Trichomycterus is described from a highland tributary of the río Meta (Orinoco basin), along the east flank of Páramo de Cruz Verde, Eastern Cordillera of Colombia. The new species is distinguished from most of its congeners by having a reduced posterior cranial fontanel, restricted to the parieto-supraoccipital, cleithrum pierced by several foramina, and an unique combination of four irregular rows of conic teeth in premaxilla and dentary, 13-14 opercular odontodes, 41-43 interopercular odontodes, 6-7 branchiostegal rays, 40 or 41 free vertebrae, 14-18 ribs, first ray of pectoral fin slightly projected as a short filament, 7-8 branched pectoral-fin rays, dorsal-fin origin at same level of pelvic-fin insertion, anal-fin origin posterior to dorsal-fin base, caudal-fin margin slightly rounded, a single upper hypural plate (3+4+5), and coloration pattern consisting in ground color dark brown with a thin mid-lateral dark stripe. Phylogenetic relationships of the new species based on the shared presence of derived features related to posterior cranial fontanel and cleithrum are discussed. The new species is also compared to the only two described species from Andean tributaries of río Orinoco basin.

Baculoviruses (Baculoviridae) are double-stranded DNA viruses which infect the larval stages of insects belonging to the orders Lepidoptera, Hymenoptera and Diptera. Due to their narrow host range and high virulence to target insects, different baculoviruses have been used as biological control agents in pest control. Severe soil pests of many agricultural and horticultural crops, which are difficult to be controlled, are larvae of the genus Agrotis (Lepidoptera: Noctuidae), also called cutworms. Their habitat is the soil or soil surface where they feed on seedlings, stems, and other parts of plants. So far, cutworms are mainly control by chemical pesticides, but biological control agents would be highly desirable for environmental reasons. Two of the most important cutworm pests are the common cutworm, Agrotis segetum (Denis & Schiffermuller), and the black cutworm, A. ipsilon (Hufnagel). At least four distinct baculovirus species, three of the genus Alphabaculovirus and one of the genus Betabaculovirus, were isolated from these two cutworm species. The alphabaculoviruses are the Agrotis segetum nucleopolyhedrovirus A (AgseNPV-A), Agrotis segetum nucleopolyhedrovirus B (AgseNPV-B), and Agrotis ipsilon nucleopolyhedrovirus (AgipNPV). The Agrotis segetum granulovirus (AgseGV) represents the betabaculovirus. Together with their two host species, from which they were first isolated and characterized, they form the so-called Agrotis baculovirus complex. Agrotis baculoviruses have the potential to be used as biological control agents for the control of Agrotis cutworms. However, in-depth knowledge and a full characterization of their biology, molecular setup, and virulence parameters are required for a successful registration and application in the field. In this study the genome sequence of AgseNPV-B was fully sequenced. Its genome is 148,981 bp in length and codes for 150 putative open reading frames. Whole genome comparisons with AgseNPV-A and AgipNPV, whose genome sequences have been published previously, suggested that AgseNPV-B belongs to a new species of the Agrotis baculovirus complex. Phylogenetic analysis indicated a very close relationship to AgipNPV and it could be concluded that both viruses are two distinct species at an early stage of separation. Whole genome alignments revealed a different number of viral enhancing factor (vef) gene copies in AgseNPV-A, AgseNPV-B and AgipNPV as one of the most striking distinguishing features between their genomes. VEFs are known to affect the virulence of baculoviruses. A putative site of genomic recombination was found in the region of the cathepsin and chitinase genes where the high co-linearity of the genomes of all three Agrotis nucleopolyhedroviruses was interrupted by inversions, deletions, or insertions. A putative fifth Agrotis baculovirus, the Agrotis exclamationis nucleopolyhedrovirus (AgexNPV), was suggested to be an isolate of AgseNPV-B due to high nucleotide sequence similarities of partial genomic regions. Based on the genome sequences of AgseNPV-A, AgseNPV-B, AgipNPV and AgseGV a multiplex PCR based method for the identification of these Agrotis baculoviruses was established. Highly specific oligonucleotide primers specific for the polyhedrin (polh) or granulin (gran) genes of the four viruses were developed and resulted in discriminating PCR fragments. Furthermore, this method allowed the quantitation of AgseGV and AgseNPV-B by quantitative PCR (qPCR). Since co-infections of AgseGV and AgseNPV-B have been observed and a combination of both viruses was considered as a combined biological control agent, the potential interaction of both viruses in mixed infections was investigated. Potential interactions between AgseNPV-B and AgseGV were examined in activity studies using single virus as well as combined virus infections of neonate A. segetum larvae. Mortality rates were determined and the virus progeny produced in individual larvae was quantified by using the newly established qPCR method of quantitation of AgseNPV-B and AgseGV. As a result, combinations of AgseNPV-B and AgseGV did not exhibit an advantageous effect in terms of pest control. Neither an increase in mortality rates in mixed virus treatments in comparison with single virus treatments, nor an increase in production of AgseNPV-B or AgseGV progeny in coinfected larvae was observed. On the contrary, a competitive behavior of both viruses in mixed infections could be concluded. The present thesis contribute to the biological control of Agrotis cutworms by providing extensive insight into the molecular setup of these viruses and the characterization of AgseNPV-B as a new Alphabaculovirus species. The use and registration of baculoviruses as biocontrol agents rely on such virus characterizations as well as on virus activity studies that were performed for AgseNPV-B and AgseGV. The new technique in Agrotis baculovirus detection and quantitation will facilitate future single and mixed infection studies of AgseNPV-B and AgseGV, as well as other combinations of Agrotis baculoviruses. Auf Wunsch des Autors / der Autorin ist diese Dissertation nur als Druckausgabe verfugbar.

Shadwick, Lora L., Brown, Matthew W., Tice, Alexander K., Spiegel, Frederick W. (2016): A New Amoeba with Protosteloid Fruiting: Luapeleamoeba hula n. g. n. sp. (Acanthamoebidae, Centramoebida, Amoebozoa). Acta Protozoologica 55 (3): 123-134, DOI: 10.4467/16890027AP.16.012.5744, URL: https://www.mendeley.com/catalogue/865f014f-9b4c-3650-8099-18274e46c1e2/