Vicariance and dispersal in southern hemisphere freshwater fish clades: a palaeontological perspective

Fossils indicate marine dispersal in osteoglossid fishes, a classic example of continental vicariance

The separation of closely related terrestrial or freshwater species by vast marine barriers represents a biogeographical riddle. Such cases can provide evidence for vicariance, a process whereby ancient geological events like continental rifting divided ancestral geographical ranges. With an evolutionary history extending tens of millions of years, freshwater ecology, and distribution encompassing widely separated southern landmasses, osteoglossid bonytongue fishes are a textbook case of vicariance attributed to Mesozoic fragmentation of the Gondwanan supercontinent. Largely overlooked fossils complicate the clean narrative invoked for extant species by recording occurrences on additional continents and in marine settings. Here, we present a new total-evidence phylogenetic hypothesis for bonytongue fishes combined with quantitative models of range evolution and show that the last common ancestor of extant osteoglossids was likely marine, and that the group colonized freshwater settings at least four times when both extant and extinct lineages are considered. The correspondence between extant osteoglossid relationships and patterns of continental fragmentation therefore represents a striking example of biogeographical pseudocongruence. Contrary to arguments against vicariance hypotheses that rely only on temporal or phylogenetic evidence, these results provide direct palaeontological support for enhanced dispersal ability early in the history of a group with widely separated distributions in the modern day.

Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes

BACKGROUND

To 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.

RESULTS

We 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.

CONCLUSIONS

The 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.

Major shifts in biogeographic regions of freshwater fishes as evidence of the Anthropocene epoch

Animals and plants worldwide are structured in global biogeographic regions, which were shaped by major geologic forces during Earth history. Recently, humans have changed the course of events by multiplying global pathways of introduction for nonindigenous species and propagating local species extirpations. Here, we report on how introductions and extirpations have changed the distributions of freshwater fishes worldwide and how it affected their natural biogeographic regions. We found major shifts in natural regions, with the emergence of an intercontinental region arising from the fusion of multiple faunas, which we named Pan-Anthropocenian Global North and East Asia (PAGNEA). The PAGNEA region is evocative of the Pangea supercontinent, as flows of introductions show that dispersal has become possible again across multiple continents, suggesting that human activities have superseded natural geological forces. Our results constitute evidence on the expected modification of biostratigraphic boundaries based on freshwater fish, which are abundant in the fossil record, thereby supporting the concept of the Anthropocene epoch.

Reassessing a cryptic history of early trilobite evolution

Trilobites are an iconic Paleozoic group of biomineralizing marine euarthropods that appear abruptly in the fossil record (c. 521 million years ago) during the Cambrian ‘explosion’. This sudden appearance has proven controversial ever since Darwin puzzled over the lack of pre-trilobitic fossils in the Origin of Species, and it has generally been assumed that trilobites must have an unobserved cryptic evolutionary history reaching back into the Precambrian. Here we review the assumptions behind this model, and suggest that a cryptic history creates significant difficulties, including the invocation of rampant convergent evolution of biomineralized structures and the abandonment of the synapomorphies uniting the clade. We show that a vicariance explanation for early Cambrian trilobite palaeobiogeographic patterns is inconsistent with factors controlling extant marine invertebrate distributions, including the increasingly-recognized importance of long-distance dispersal. We suggest that survivorship bias may explain the initial rapid diversification of trilobites, and conclude that the group’s appearance at c. 521 Ma closely reflects their evolutionary origins.

A reassessment of early trilobite phylogenetic relationships and palaeobiogeographic patterns suggests that a cryptic evolutionary history is unlikely for this group. The abrupt appearance of trilobites is likely to closely reflect their evolutionary origins, and may be explained by survivorship biases inherent in the fossil record.

Biogeography and eye size evolution of the ogre-faced spiders

Net-casting spiders (Deinopidae) comprise a charismatic family with an enigmatic evolutionary history. There are 67 described species of deinopids, placed among three genera, Deinopis, Menneus, and Asianopis, that are distributed globally throughout the tropics and subtropics. Deinopis and Asianopis, the ogre-faced spiders, are best known for their giant light-capturing posterior median eyes (PME), whereas Menneus does not have enlarged PMEs. Molecular phylogenetic studies have revealed discordance between morphology and molecular data. We employed a character-rich ultra-conserved element (UCE) dataset and a taxon-rich cytochrome-oxidase I (COI) dataset to reconstruct a genus-level phylogeny of Deinopidae, aiming to investigate the group's historical biogeography, and examine PME size evolution. Although the phylogenetic results support the monophyly of Menneus and the single reduction of PME size in deinopids, these data also show that Deinopis is not monophyletic. Consequently, we formally transfer 24 Deinopis species to Asianopis; the transfers comprise all of the African, Australian, South Pacific, and a subset of Central American and Mexican species. Following the divergence of Eastern and Western deinopids in the Cretaceous, Deinopis/Asianopis dispersed from Africa, through Asia and into Australia with its biogeographic history reflecting separation of Western Gondwana as well as long-distance dispersal events.

Phylogenomics of bonytongue fishes (Osteoglossomorpha) shed light on the craniofacial evolution and biogeography of the weakly electric clade Mormyridae

Bonytongues (Osteoglossomorpha) constitute an ancient clade of teleost fishes distributed in freshwater habitats throughout the world. The group includes well-known species such as arowanas, featherbacks, pirarucus, and the weakly electric fishes in the family Mormyridae. Their disjunct distribution, extreme morphologies, and electrolocating capabilities (Gymnarchidae and Mormyridae) have attracted much scientific interest, but a comprehensive phylogenetic framework for comparative analysis is missing, especially for the species-rich family Mormyridae. Of particular interest are disparate craniofacial morphologies among mormyrids which might constitute an exceptional model system to study convergent evolution. We present a phylogenomic analysis based on 546 exons of 179 species (out of 260), 28 out of 29 genera, and all six families of extant bonytongues. Based on a recent reassessment of the fossil record of osteoglossomorphs, we inferred dates of divergence among trans-continental clades and the major groups. The estimated ages of divergence among extant taxa (e.g., Osteoglossomorpha, Osteoglossiformes, Mormyroidea) are older than previous reports, but most of the divergence dates obtained for clades on separate continents are too young to be explained by simple vicariance hypotheses. Biogeographic analysis of mormyrids indicates that their high species diversity in the Congo Basin is a consequence of range reductions of previously widespread ancestors and that the highest diversity of craniofacial morphologies among mormyrids originated in this basin. Special emphasis on a taxon-rich representation for mormyrids revealed pervasive misalignment between our phylogenomic results and mormyrid taxonomy due to repeated instances of convergence for extreme craniofacial morphologies. Estimation of ancestral phenotypes revealed contingent evolution of snout elongation and unique projections from the lower jaw to form the distinctive Schnauzenorgan. Synthesis of comparative analyses suggests that the remarkable craniofacial morphologies of mormyrids evolved convergently due to niche partitioning, likely enabled by interactions between their exclusive morphological and electrosensory adaptations.

Phylogeography of high Andean killifishes Orestias (Teleostei: Cyprinodontidae) in Caquena and Lauca sub-basins of the Altiplano (Chile): mitochondrial and nuclear analysis of an endangered fish

From the early Miocene, the uplift of the Andes Mountains, intense volcanic activity and the occurrence of successive periods of dryness and humidity would have differentially influenced the modification of Altiplano watersheds, and consequently the evolutionary history of the taxa that live there. We analyzed Orestias populations from the Caquena and Lauca Altiplanic sub-basins of northern Chile to determine their genetic differentiation and relationship to their geographical distribution using mitochondrial (D-loop) and nuclear (microsatellite) molecular markers and to reconstruct its biogeographic history on these sub-basins. The results allowed reconstructing and reevaluating the evolutionary history of the genus in the area; genic diversity and differentiation together with different founding genetic groups suggest that Orestias have been spread homogeneously in the study area and would have experienced local disturbances that promoted isolation and diversification in restricted zones of their distribution.

A revision of Laeliichthys ancestralis Santos, 1985 (Teleostei: Osteoglossomorpha) from the Lower Cretaceous of Brazil: Phylogenetic relationships and biogeographical implications

A re-description of the freshwater, Early Cretaceous osteoglossomorph Laeliichthys ancestralis Santos, 1985, from the Sanfranciscana Basin of Brazil, is provided. New anatomical details and a revised diagnosis, as well as a new phylogeny are presented. A phylogenetic analysis places this taxon within the Osteoglossomorpha most likely as a member of the Notopteroidei. Within this clade Laeliichthys is the sister-taxon of the Notopteridae. The subfamily Laeliichthyinae is elevated to family rank. The revised phylogenetic position revealed in this study has important consequences on the biogeography of Notopteroidei as it extends their distribution to western Gondwana, prior to the separation of South America and Africa, and extends the evolutionary origins of notopteroid lineages by at least ~27 Myr before their first appearance in the fossil record.

Phenotypic and genetic differentiation between diadromous and landlocked puyen Galaxias maculatus

This study reports the phenotypic and genetic differences between individuals of puyen Galaxias maculatus from two sites in the same river basin in Tierra del Fuego National Park, southern South America. Individuals from the two sampling sites presented morphometric and genetic differences. The morphometric differences indicated that individuals from Laguna Negra (LN) were short and more robust and had large eyes, whereas those from Arroyo Negro (AN) were thin and elongated and had small eyes. Genetic differences showed that AN individuals had a greater genetic structuration and an older demographic history than LN individuals. The results of this study affirmed that the individuals from the two sampling sites belong to different populations with a high degree of isolation. The demographic history could indicate that the individuals of G. maculatus which migrated to northern areas during the last glaciation settled in the Beagle Channel after its formation. The LN population could have originated after the retreat of the glaciers, migrating from AN.

Deciphering the Evolutionary History of Arowana Fishes (Teleostei, Osteoglossiformes, Osteoglossidae): Insight from Comparative Cytogenomics

Arowanas (Osteoglossinae) are charismatic freshwater fishes with six species and two genera (Osteoglossum and Scleropages) distributed in South America, Asia, and Australia. In an attempt to provide a better assessment of the processes shaping their evolution, we employed a set of cytogenetic and genomic approaches, including i) molecular cytogenetic analyses using C- and CMA₃/DAPI staining, repetitive DNA mapping, comparative genomic hybridization (CGH), and Zoo-FISH, along with ii) the genotypic analyses of single nucleotide polymorphisms (SNPs) generated by diversity array technology sequencing (DArTseq). We observed diploid chromosome numbers of 2n = 56 and 54 in O. bicirrhosum and O. ferreirai, respectively, and 2n = 50 in S. formosus, while S. jardinii and S. leichardti presented 2n = 48 and 44, respectively. A time-calibrated phylogenetic tree revealed that Osteoglossum and Scleropages divergence occurred approximately 50 million years ago (MYA), at the time of the final separation of Australia and South America (with Antarctica). Asian S. formosus and Australian Scleropages diverged about 35.5 MYA, substantially after the latest terrestrial connection between Australia and Southeast Asia through the Indian plate movement. Our combined data provided a comprehensive perspective of the cytogenomic diversity and evolution of arowana species on a timescale.

Into Africa via docked India: a fossil climbing perch from the Oligocene of Tibet helps solve the anabantid biogeographical puzzle

The northward drift of the Indian Plate and its collision with Eurasia have profoundly impacted the evolutionary history of the terrestrial organisms, especially the ones along the Indian Ocean rim. Climbing perches (Anabantidae) are primary freshwater fishes showing a disjunct south Asian-African distribution, but with an elusive paleobiogeographic history due to the lack of fossil evidence. Here, based on an updated time-calibrated anabantiform phylogeny integrating a number of relevant fossils, the divergence between Asian and African climbing perches is estimated to have occurred in the middle Eocene (ca. 40 Ma, Ma: million years ago), a time when India had already joined with Eurasia. The key fossil lineage is †Eoanabas, the oldest anabantid known so far, from the upper Oligocene of the Tibetan Plateau. Ancestral range reconstructions suggest a Southeast Asian origin in the early Eocene (ca. 48 Ma) and subsequent dispersals to Tibet and then India for this group. Thereby we propose their westbound dispersal to Africa via the biotic bridge between India and Africa. If so, climbing perch precursors had probably followed the paleobiogeographical route of snakehead fishes, which have a slightly older divergence between African and Asian taxa. As such, our study echoes some recent molecular analyses in rejecting the previously held "Gondwana continental drift vicariance" or late Mesozoic dispersal scenarios for the climbing perches, but provides a unique biogeographical model to highlight the role of the pre-uplift Tibet and the docked India in shaping the disjunct distribution of some air-breathing freshwater fishes around the Indian Ocean.