Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species

Ancient and Recent Hybridization in the Oreochromis Cichlid Fishes

Cichlid fishes of the genus Oreochromis (tilapia) are among the most important fish for inland capture fisheries and global aquaculture. Deliberate introductions of non-native species for fisheries improvement and accidental escapees from farms have resulted in admixture with indigenous species. Such hybridization may be detrimental to native biodiversity, potentially leading to genomic homogenization of populations and the loss of important genetic material associated with local adaptation. By contrast, introgression may fuel diversification when combined with ecological opportunity, by supplying novel genetic combinations. To date, the role of introgression in the evolutionary history of tilapia has not been explored. Here we studied both ancient and recent hybridization in tilapia, using whole genome resequencing of 575 individuals from 23 species. We focused on Tanzania, a natural hotspot of tilapia diversity, and a country where hybridization between exotic and native species in the natural environment has been previously reported. We reconstruct the first genome-scale phylogeny of the genus and reveal prevalent ancient gene flow across the Oreochromis phylogeny. This has likely resulted in the hybrid speciation of one species, O. chungruruensis. We identify multiple cases of recent hybridization between native and introduced species in the wild, linked to the use of non-native species in both capture fisheries improvement and aquaculture. This has potential implications for both conservation of wild populations and the development of the global tilapia aquaculture industry.

Freshwater fishes of Israel; a revised and updated annotated checklist2023

The current status of the freshwater fishes of Israel is revised, and an updated checklist is presented. The confirmed freshwater fishes of Israel comprise 55 species belonging to nine orders, 14 families, and 39 genera. Among these, 19 species (34.6%) are alien, and four species (7.3%) are considered endemic to Israel. The orders with the largest numbers of species in the ichthyofauna of Israel are Cypriniformes (19 species), followed by Cichliformes (14 species), Cyprinodontiformes (seven species), Mugiliformes (six species), Siluriformes (four species), Salmoniformes (two species), and the others represent one species in each. At the family level, the Cichlidae have the greatest number of species (14 species; 25.5% of the total species), followed by Cyprinidae (10 species), Leuciscidae and Mugilidae (six species in each), Aphaniidae (four species), Nemacheilidae and Poecilidae (three species in each). According to IUCN Red List criteria, among 36 naturally distributed species (alien species not included), two species are extinct (EX) and nine species (25.0%) are categorized as threatened extinctions, with two (5.6%) CR, four (11.1%) EN, and three (8.3%) VU.

Ancient DNA is preserved in fish fossils from tropical lake sediments

Tropical freshwater lakes are well known for their high biodiversity, and particularly the East African Great Lakes are renowned for their adaptive radiation of cichlid fishes. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, little is known about evolutionary trajectories within lineages, the impacts of environmental drivers, or the scope and nature of now-extinct diversity. Time-structured palaeodata from geologically young fossil records, such as fossil counts and particularly ancient DNA (aDNA) data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous aDNA. Despite generally low endogenous content and high sample dropout, the application of high-throughput sequencing and, in some cases, sequence capture allowed taxonomic assignment and phylogenetic placement of 17% of analysed fish fossils to family or tribe level, including remains which are up to 2700 years old or weigh less than 1 mg. The relationship between aDNA degradation and the thermal age of samples is similar to that described for terrestrial samples from cold environments when adjusted for elevated temperature. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in bottom water oxygenation. Our study demonstrates that the sediment records of tropical lakes can preserve genetic information on rapidly diversifying fish taxa over time scales of millennia.

Contemporary perspectives on the ecological impacts of invasive freshwater fishes

Introductions of non-native freshwater fish continue to increase globally, although only a small proportion of these introductions will result in an invasion. These invasive populations can cause ecological impacts in the receiving ecosystem through processes including increased competition and predation pressure, genetic introgression and the transmission of non-native pathogens. Definitions of ecological impact emphasize that shifts in the strength of these processes are insufficient for characterizing impact alone and, instead, must be associated with a quantifiable decline of biological and/or genetic diversity and lead to a measurable loss of diversity or change in ecosystem functioning. Assessments of ecological impact should thus consider the multiple processes and effects that potentially occur from invasive fish populations where, for example, impacts of invasive common carp Cyprinus carpio populations are through a combination of bottom-up and top-down processes that, in entirety, cause shifts in lake stable states and decreased species richness and/or abundances in the biotic communities. Such far-reaching ecological impacts also align to contemporary definitions of ecosystem collapse, given they involve substantial and persistent declines in biodiversity and ecosystem functions that cannot be recovered unaided. Thus, while not all introduced freshwater fishes will become invasive, those species that do develop invasive populations can cause substantial ecological impacts, where some of the impacts on biodiversity and ecosystem functioning might be sufficiently harmful to be considered as contributing to ecosystem collapse.

Master-Key Regulators of Sex Determination in Fish and Other Vertebrates-A Review

In vertebrates, mainly single genes with an allele ratio of 1:1 trigger sex-determination (SD), leading to initial equal sex-ratios. Such genes are designated master-key regulators (MKRs) and are frequently associated with DNA structural variations, such as copy-number variation and null-alleles. Most MKR knowledge comes from fish, especially cichlids, which serve as a genetic model for SD. We list 14 MKRs, of which dmrt1 has been identified in taxonomically distant species such as birds and fish. The identification of MKRs with known involvement in SD, such as amh and fshr, indicates that a common network drives SD. We illustrate a network that affects estrogen/androgen equilibrium, suggesting that structural variation may exert over-expression of the gene and thus form an MKR. However, the reason why certain factors constitute MKRs, whereas others do not is unclear. The limited number of conserved MKRs suggests that their heterologous sequences could be used as targets in future searches for MKRs of additional species. Sex-specific mortality, sex reversal, the role of temperature in SD, and multigenic SD are examined, claiming that these phenomena are often consequences of artificial hybridization. We discuss the essentiality of taxonomic authentication of species to validate purebred origin before MKR searches.

Absence of Figla-like Gene Is Concordant with Femaleness in Cichlids Harboring the LG1 Sex-Determination System

Oreochromis niloticus has been used as a reference genome for studies of tilapia sex determination (SD) revealing segregating genetic loci on linkage groups (LGs) 1, 3, and 23. The master key regulator genes (MKR) underlying the SD regions on LGs 3 and 23 have been already found. To identify the MKR in fish that segregate for the LG1 XX/XY SD-system, we applied short variant discovery within the sequence reads of the genomic libraries of the Amherst hybrid stock, Coptodon zillii and Sarotherodon galilaeus, which were aligned to a 3-Mbp-region of the O. aureus genome. We obtained 66,372 variants of which six were concordant with the XX/XY model of SD and were conserved across these species, disclosing the male specific figla-like gene. We further validated this observation in O. mossambicus and in the Chitralada hybrid stock. Genome alignment of the 1252-bp transcript showed that the figla-like gene’s size was 2664 bp, and that its three exons were capable of encoding 99 amino acids including a 45-amino-acid basic helix–loop–helix domain that is typical of the ovary development regulator—factor-in-the-germline-alpha (FIGLA). In Amherst gonads, the figla-like gene was exclusively expressed in testes. Thus, the figla-like genomic presence determines male fate by interrupting the female developmental program. This indicates that the figla-like gene is the long-sought SD MKR on LG1.

Mosaic or melting pot: The use of monogeneans as a biological tag and magnifying glass to discriminate introduced populations of Nile tilapia in sub-Saharan Africa

The origin of introduced Nile tilapia stocks in sub-Saharan Africa is largely unknown. In this study, the potential of monogeneans as a biological tag and magnifying glass is tested to reveal their hosts' stocking history. The monogenean gill community of different Nile tilapia populations in sub-Saharan Africa was explored, and a phylogeographic analysis was performed based on the mitogenomes of four dactylogyrid species (Cichlidogyrus halli, C. sclerosus, C. thurstonae, and Scutogyrus longicornis). Our results encourage the use of dactylogyrids as biological tags. The magnifying glass hypothesis is only confirmed for C. thurstonae, highlighting the importance of the absence of other potential hosts as prerequisites for a parasite to act as a magnifying glass. With the data generated here, we are the first to extract mitogenomes from individual monogeneans and to perform an upscaled survey of the comparative phylogeography of several monogenean species with unprecedented diagnostic resolution.

Population genomics of introduced Nile tilapia Oreochromis niloticus (Linnaeus, 1758) in the Democratic Republic of the Congo: Repeated introductions since colonial times with multiple sources

During colonial times, Nile tilapia Oreochromis niloticus (Linnaeus, 1758) was introduced into non-native parts of the Congo Basin (Democratic Republic of the Congo, DRC) for the first time. Currently, it is the most farmed cichlid in the DRC, and is present throughout the Congo Basin. Although Nile tilapia has been reported as an invasive species, documentation of historical introductions into this basin and its consequences are scant. Here, we study the genetic consequences of these introductions by genotyping 213 Nile tilapia from native and introduced regions, focusing on the Congo Basin. Additionally, 48 specimens from 16 other tilapia species were included to test for hybridization. Using RAD sequencing (27,611 single nucleotide polymorphisms), we discovered genetic admixture with other tilapia species in several morphologically identified Nile tilapia from the Congo Basin, reflecting their ability to interbreed and the potential threat they pose to the genetic integrity of native tilapias. Nile tilapia populations from the Upper Congo and those from the Middle-Lower Congo are strongly differentiated. The former show genetic similarity to Nile tilapia from the White Nile, while specimens from the Benue Basin and Lake Kariba are similar to Nile tilapia from the Middle-Lower Congo, suggesting independent introductions using different sources. We conclude that the presence of Nile tilapia in the Congo Basin results from independent introductions, reflecting the dynamic aquaculture history, and that their introduction probably leads to genetic interactions with native tilapias, which could lower their fitness. We therefore urge avoiding further introductions of Nile tilapia in non-native regions and to use native tilapias in future aquaculture efforts.

Right out of the gate: the genomics of Lessepsian invaders in the vicinity of the Suez Canal

Marine organisms that enter the Mediterranean from the Red Sea via the Suez Canal are known as Lessepsian bioinvaders. In general, genetic studies of Lessepsian fishes have shown little structure between Red Sea and Mediterranean populations. Yet notable exceptions suggest the importance of life-history factors that may influence patterns of spatial genetic variation. In this study, by sampling two invasive fishes with different life histories (the rabbitfish Siganus rivulatus and the filefish Stephanolepis diaspros), we looked at evidence of population structure and selection at the boundary between the Red Sea and the Mediterranean (the Suez Canal), using thousands of molecular markers. Results illustrate two divergent patterns of genetic patterns, with little genetic structure in S. rivulatus and strong population structure in S. diaspros, even at such small spatial scale. We discuss differences in ecological characteristics between the two species to account for such differences. In addition, we report that in the face of both high (S. rivulatus) and low (S. diaspros) gene flow, loci under selection were uncovered, and some protein coding genes were identified as being involved with osmoregulation, which seems to be an important feature of individuals crossing the salinity-variable Suez Canal. The presence of genes under selection in populations near the Suez Canal supports the idea that selection may be active and essential for successful invasions right out of the gate.

Quantifying nonlinear temporal effects of ethanol preservation on round goby (Neogobius melanostomus) anatomical traits

Geometric morphometrics provides a powerful means of evaluating differences in phenotypic traits among specimens. However, inferences of trait variability can be confounded when measurements are based on preserved samples. We evaluated effects of ethanol preservation on morphology over a 22-week time period for a Laurentian Great Lakes invasive fish, round goby (Neogobius melanostomus, Pallas 1814), using sets of 17 lateral and six dorsal landmarks. We tested whether ethanol preservation affected the magnitude of inter-population variation between individuals collected from lake and river habitats. Generalized least square regression determined that length did not significantly vary through the preservation time series for fish from either population, while mass decreased significantly. Body shape variation was summarized using principal component analysis, which revealed that most preservation-associated changes occurred in the first 14 days. The lateral shape experienced a large magnitude change during the first 24 h in ethanol then only minor changes for the remainder of the study. The dorsal shape began to revert to pre-preservation measurements about 14 days following preservation. Additionally, differences in shape were apparent between the two populations throughout the experiment; however, the magnitude of differences between populations varied depending on whether dorsal or lateral landmarks were considered. Our study demonstrates that tissue responses to ethanol preservation can be more complex than a simple loss of mass, resulting in difficult to predict consequences for geometric morphometric analyses, including variable responses depending on the anatomical region being analyzed.