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The closure of the Isthmus of Panama has long been considered to be one of the best defined biogeographic calibration points for molecular divergence-time estimation. However, geological and biological evidence has recently cast doubt on the presumed timing of the initial isthmus closure around 3 Ma but has instead suggested the existence of temporary land bridges as early as the Middle or Late Miocene. The biological evidence supporting these earlier land bridges was based either on only few molecular markers or on concatenation of genome-wide sequence data, an approach that is known to result in potentially misleading branch lengths and divergence times, which could compromise the reliability of this evidence. To allow divergence-time estimation with genomic data using the more appropriate multispecies coalescent (MSC) model, we here develop a new method combining the single-nucleotide polymorphism-based Bayesian species-tree inference of the software SNAPP with a molecular clock model that can be calibrated with fossil or biogeographic constraints. We validate our approach with simulations and use our method to reanalyze genomic data of Neotropical army ants (Dorylinae) that previously supported divergence times of Central and South American populations before the isthmus closure around 3 Ma. Our reanalysis with the MSC model shifts all of these divergence times to ages younger than 3 Ma, suggesting that the older estimates supporting the earlier existence of temporary land bridges were artifacts resulting at least partially from the use of concatenation. We then apply our method to a new restriction-site associated DNA-sequencing data set of Neotropical sea catfishes (Ariidae) and calibrate their species tree with extensive information from the fossil record. We identify a series of divergences between groups of Caribbean and Pacific sea catfishes around 10 Ma, indicating that processes related to the emergence of the isthmus led to vicariant speciation already in the Late Miocene, millions of years before the final isthmus closure.

The family Trichomycteridae is one of the most diverse groups of freshwater catfishes in South and Central America with eight subfamilies, 41 genera and more than 300 valid species. Its members are widely distributed throughout South America, reaching Costa Rica in Central America and are recognized by extraordinary anatomical specializations and trophic diversity. In order to assess the phylogenetic relationships of Trichomycteridae, we collected sequence data from ultraconserved elements (UCEs) of the genome from 141 specimens of Trichomycteridae and 12 outgroup species. We used a concatenated matrix to assess the phylogenetic relationships by Bayesian inference (BI) and maximum likelihood (ML) searches and a coalescent analysis of species trees. The results show a highly resolved phylogeny with broad agreement among the three distinct analyses, providing overwhelming support for the monophyletic status of subfamily Trichomycterinae including Ituglanis and Scleronema . Previous relationship hypotheses among subfamilies are strongly corroborated, such as the sister relationship between Copionodontinae and Trichogeninae forming a sister clade to the remaining trichomycterids and the intrafamilial clade TSVSG (Tridentinae-Stegophilinae-Vandelliinae-Sarcoglanidinae-Glanapteryginae). Monophyly of Glanapteryginae and Sarcoglanidinae was not supported and the enigmatic Potamoglanis is placed outside Tridentinae.

A very significant part of the world's freshwater ichthyofauna is represented by ancient, exceptionally diverse and cosmopolitan ray-finned teleosts of the order Siluriformes. Over the years, catfish have been established as an exemplary model for probing historical biogeography at various scales. Yet, several tantalizing gaps still exist in their phylogenetic history, timeline and mode of diversification. Here, we re-examine the phylogeny of catfish by assembling and analyzing almost all publicly available mitogenome data. We constructed an ingroup matrix of 62 full-length mitogenome sequences from 20 catfish families together with four cypriniform outgroups, spanning 15,557 positions in total. Partitioned maximum likelihood analyses and Bayesian relaxed clock dating using fossil age constraints provide some useful and novel insights into the evolutionary history of this group. Loricarioidei are recovered as the first siluriform group to diversify, rendering Neotropics the cradle of the order. The next deepest clade is the South American Diplomystoidei placed as a sister group to all the remaining Siluroidei. The two multifamilial clades of \"Big Asia\" and \"Big Africa\" are also recovered, albeit nodal support for the latter is poor. Within \"Big Asia\", Bagridae are clearly polyphyletic. Other interfamilial relationships, including Clariidae + Heteropneustidae, Doradidae + Auchenipteridae and Ictaluridae + Cranoglanididae are robustly resolved. Our chronogram shows that siluriforms have a Pangaean origin, at least as far back as the Early Cretaceous. The inferred timeline of the basal splits corroborates the \"Out-of-South America\" hypothesis and accords well with the fossil record. The divergence of Siluroidei most likely postdated the final separation of Africa and South America. An appealing case of phylogenetic affinity elaborated by biogeographic dispersal is exemplified by the Early Paleogene split between the Southeast Asian Cranoglanididae and Ictaluridae, with the latter radiating into North America's freshwater realm by Eocene. The end of Cretaceous probably concludes the major bout of diversification at the family level while with the dawn of the Cenozoic a prolific radiation is evident at the generic level.

The order Siluriformes (catfish) is one of the largest groups of fish. Diversity in the body size among its species, which range from a few centimeters to 4 meters, makes Siluriformes an interesting group to investigate the body size evolution. Here, we present the complete mitogenome of Brachyplatystoma filamentosum (Piraíba), the largest Amazonian catfish, to explore the evolutionary history of Siluriformes and their body size dynamics. The Piraíba’s mtDNA is 16,566 bp long, with a GC content of 42.21% and a D-loop of 911 bp. Phylogenetic analysis was conducted using protein-coding sequences, tRNAs, and rRNAs from mtDNA of Piraíba and 137 other Siluriformes species. Time-calibrated maximum likelihood trees estimated the origin of the order Siluriformes to be ~118.4 Ma, with the Loricarioidei suborder diversifying first, followed by Diplomystoidei and Siluroidei. The Siluroidei suborder experienced rapid expansion around 94.1 Ma. Evolutionary dynamics revealed 16 positive and 11 negative directional body size changes in Siluriformes, with no global trend toward larger or smaller sizes, and with Piraíba showing a significant size increase (5.65 times over 40.8 Ma). We discuss how biological, ecological and environmental factors could have shaped the evolution of body size in this group.

Abstract The sand catfish or painted catfish (Hypostomus affinis) is a species native to Brazil and has some peculiar characteristics: a flattened body covered by bony plates and fins with spikes for fixing on rocks. Molecular studies have been carried out to better understand this and other species of fish. In this study, a comparison was made between DNA extraction methodologies to define the best extraction protocol for this species. For the study, approximately two grams of the caudal fin of twenty adult specimens of Hypostomus affinis were used for DNA extraction. For this, three extraction protocols were performed. The quantification of the genetic material was carried out in a NanoDrop 2000c Spectrophotometer, thus obtaining the DNA concentration in ng/µL and purity of each sample (A260/A280 and 230/260 ratio). Protocol I, based on Barrero, was the one that presented the best result of DNA concentration of 2846.28 ng/µL. Showing no difference from the III NaCL, which showed 2385.69 ng/µL of DNA. It is concluded that the protocol I presented the best results in terms of quantity and purity. Resumo O bagre-da-areia ou bagre-pintado (Hypostomus affinis) é uma espécie nativa do Brasil e possui algumas características peculiares: corpo achatado coberto por placas ósseas e nadadeiras com espinhos para fixação nas rochas. Estudos moleculares têm sido realizados para melhor compreender esta e outras espécies de peixes. Neste estudo foi feita uma comparação entre metodologias de extração de DNA, para definir o melhor protocolo de extração para esta espécie. Para o estudo, foram utilizados aproximadamente dois gramas da nadadeira caudal de vinte espécimes adultos de Hypostomus affinis para extração de DNA. Para isso, foram realizados três protocolos de extração. A quantificação do material genético foi realizada em Espectrofotômetro NanoDrop 2000c, obtendo-se assim a concentração de DNA em ng/µL e a pureza de cada amostra (relação A260/A280 e 230/260). O protocolo I baseado em Barrero, foi o que apresentou melhor resultado de concentração de DNA 2846,28 ng/µL. Não apresentando diferença em relação ao III NaCL, que apresentou 2385,69 ng/µL de DNA. Conclui-se que o protocolo I apresentou os melhores resultados em termos de quantidade e pureza.

Background Freshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp.) and is currently distributed throughout the world's continents except Antarctica. Despite such remarkable species diversity and ubiquity, the evolutionary history of this major freshwater fish clade, Otophysi, remains largely unexplored. To gain insight into the history of otophysan diversification, we constructed a timetree based on whole mitogenome sequences across 110 species representing 55 of the 64 families. Results Partitioned maximum likelihood analysis based on unambiguously aligned sequences (9923 bp) confidently recovered the monophyly of Otophysi and the two constituent subgroups (Cypriniformes and Characiphysi). The latter clade comprised three orders (Gymnotiformes, Characiformes, Siluriformes), and Gymnotiformes was sister to the latter two groups. One of the two suborders in Characiformes (Characoidei) was more closely related to Siluriformes than to its own suborder (Citharinoidei), rendering the characiforms paraphyletic. Although this novel relationship did not receive strong statistical support, it was supported by analyzing independent nuclear markers. A relaxed molecular clock Bayesian analysis of the divergence times and reconstruction of ancestral habitats on the timetree suggest a Pangaean origin and Mesozoic radiation of otophysans. Conclusions The present timetree demonstrates that survival of the ancestral lineages through the two consecutive mass extinctions on Pangaea, and subsequent radiations during the Jurassic through early Cretaceous shaped the modern familial diversity of otophysans. This evolutionary scenario is consistent with recent arguments based on biogeographic inferences and molecular divergence time estimates. No fossil otophysan, however, has been recorded before the Albian, the early Cretaceous 100-112 Ma, creating an over 100 million year time span without fossil evidence. This formidable ghost range partially reflects a genuine difference between the estimated ages of stem group origin (molecular divergence time) and crown group morphological diversification (fossil divergence time); the ghost range, however, would be filled with discoveries of older fossils that can be used as more reasonable time constraints as well as with developments of more realistic models that capture the rates of molecular sequences accurately.

Abstract The study estimated the risk associated with the consumption of five large migratory catfish species for the health of the most vulnerable population, identifying the total mercury and selenium concentrations, the Se/Hg molar ratio, and the Health Benefit Value for selenium (HBVSe) in fish caught in the upper Meta River (Colombia). Total mercury concentrations ranged from 0.154µgg-1 wet weight (ww) for a sample of Pseudoplatystoma fasciatum to 1.86µgg-1 ww for a sample of Pinirampus pirinampu. Forty-five percent of the Pinirampus pirinampu samples and two of the three Brachyplatystoma rousseauxii samples exceeded the reference level for mercury in saltwater predatory fish. Selenium concentrations ranged from 0.059 to 3.16µgg-1 ww. The species with the highest average selenium level was Pseudoplatystoma fasciatum, while Brachyplatystoma platynemum showed the lowest. Significant differences in Se/Hg molar ratios were found among all fish species, with Pseudoplatystoma fasciatum displaying the most favorable ratio. No linear relationship emerged between Hg and Se concentrations. The maximum allowable weekly consumption of Pseudoplatystoma fasciatum to meet the Food and Agriculture Organization (FAO)/World Health Organization (WHO) recommended Provisional Tolerable Weekly Intake (PTWI) —calculated using the average mercury concentration for females and childbearing age— amounted to 281 g and 140 g for children. In Brachyplatystoma juruense, Brachyplatystoma platynemum, and Brachyplatystoma rousseauxii, which had a Se/Hg molar ratio of less than 1 and an adverse HBVSe, the acceptable intake for this population decreases to about 100 g for females and 50 g for children, respectively. These recommended portions protect against mercury neurotoxicity and selenium deficiency, especially in the most sensitive populations. Resumo O estudo avaliou o risco asociado ao consumo de cinco espécies de bagres migratórios para a saúde da população mais vulnerável, identificando as concentrações totais de mercúrio e selênio, a relação molar Se/Hg, e o Valor de Benefício à saúde de selênio (HBVSe) em peixes capturados na cabeceira do rio Meta, Colômbia. As concentrações de Mercúrio total variaram de 0.154µgg-1 peso úmido (pu) para as amostras de Pseudoplatystoma fasciatum a 1.86µgg-1 pu para a amostra de Pinirampus pirinampu. Um total de 45% das amostras de Pinirampus pirinampu e duas das três amostras de Brachyplatystoma rousseauxii excederam os valores de referência de mercúrio em peixes predadores de água salgada. As concentrações de selênio variaram de 0.059 a 3.16µgg-1 pu. A espécie o maior nível médio de selênio foi o Pseudoplatystoma fasciatum, enquanto Brachyplatystoma platynemum apresentou o menor. Foram encontradas diferenças significativas nas razões molares de Se/Hg de todas as espécies de peixes, sendo o Pseudoplatystoma fasciatum o que apresentou a razão mais favorável. Não foi encontrada correlação positiva entre as concentrações de Hg e Se. O consumo máximo semanal permitido de Pseudoplatystoma fasciatum para atingir os Valores Semanais Provisionais Toleráveis (PTWI) recomendados pela FAO/WHO, calculados para a média da concentração de mercúrio para mulheres em idade fértil, foi 281 g e 140 g para crianças. As espécies Brachyplatystoma juruense, Brachyplatystoma platynemum e Brachyplatystoma rousseauxii, que apresentaram uma relação molar Se/Hg menor a 1 e um HBVSe adverso, a ingestão aceitável para essa população diminui aproximadamente 100 g para mulheres e 50 g para crianças, respectivamente. As porções recomendadas deveriam proteger contra a neurotoxicidade do mercúrio e da deficiência de selênio, particularmente na população mais sensível.

The genus Rineloricaria is a Neotropical freshwater fish group with a long and problematic taxonomic history, attributed to the large number of species and the pronounced similarity among them. In the present work, taxonomic information and different molecular approaches were used to identify species boundaries and characterize independent evolutionary units. We analyzed 228 samples assembled in 53 distinct morphospecies. A general mixed yule-coalescent (GMYC) analysis indicated the existence of 70 entities, while BOLD system analyses showed the existence of 56 distinct BINs. When we used a new proposed integrative taxonomy approach, mixing the results obtained by each analysis, we identified 73 OTUs. We suggest that Rineloricaria probably has some complexity in the known species and several species not formally described yet. Our data suggested that other hyperdiverse fish groups with wide distributions can be further split into many new evolutionary taxonomic units.

Background Global freshwater fishes face multiple pressures, including habitat degradation, overfishing, and environmental pollution, leading to a continuous decline in genetic diversity. Ussuri catfish ( Pseudobagrus ussuriensis , Chinese common names: Huangziang and Niuweiba) is an endemic Chinese species of considerable ecological and economic importance. Declines in population size and degradation of wild stocks have raised significant conservation and aquaculture concerns. To promote the effective conservation and sustainable use of this species’ germplasm resources, we analyzed the genetic diversity and population structure of 149 individuals from three wild populations and two cultured populations using mitochondrial genes ( Cytb and COI ) and genotyping-by-sequencing (GBS) data. These results provide a scientific basis for artificial breeding, stock enhancement, and local germplasm conservation. Results Mitochondrial analyses revealed higher genetic diversity in wild populations compared to cultured populations, with maternal lineages being relatively conserved; however, the QH and HTH populations harbored region-specific haplotypes. Population differentiation analysis indicated that the HTH population exhibits a relatively independent genetic structure. Inter-population variation based on Cytb and COI was 51.40% and 55.33%, respectively, whereas intra-population variation was relatively low. Neutrality tests suggested a recent expansion in the HLJ population, while the HTH population may have been influenced by balancing selection or a bottleneck effect. GBS sequencing yielded a total of 1,238,359 SNPs, of which 168,794 high-quality loci were retained after stringent filtering. Some SNPs (e.g., contig15925, contig70883) displayed significant allele frequency differences among populations, representing potential markers of population differentiation. The average polymorphic information content (PIC) of SNPs and InDels was low, at 0.154 and 0.147, respectively, and average nucleotide diversity (π) was 0.287 and 0.273. Most loci conformed to Hardy–Weinberg equilibrium. Genetic structure analyses revealed pronounced differentiation among populations, with the QH population exhibiting the most distinct genetic features, followed by HTH. ADMIXTURE analysis further showed that HLJ, YJ, and SC populations shared similar ancestral components, whereas HTH and QH retained relatively independent genomic signatures. Isolation-by-distance analysis indicated no significant correlation between genetic and geographic distances. Conclusion Distinct populations of P. ussuriensis exhibit pronounced genetic differentiation and region-specific haplotypes, with wild populations showing higher genetic diversity than cultured populations. We recommend prioritizing in situ conservation and germplasm purification of wild populations, and using local genetic resources preferentially in stock enhancement programs, in order to maintain genetic diversity and ensure sustainable utilization.

Background/Objectives: North African catfish (Clarias gariepinus) and bighead catfish (Clarias macrocephalus) play crucial roles in Thai aquaculture. Although significant growth disparities exist among these species, the genetic factors underlying these differences are still unknown. This study aimed to identify GH1 gene polymorphisms, in North African and bighead catfish populations across Thailand and Laos. Methods: Sequencing, phylogenetic, and clustering analyses were performed to assess genetic diversity, selection patterns, and lineage differentiation of catfish partial GH1 fragment. Results: Six alleles of the studied fragment of GH1 gene were identified; they differed at 33 variable sites within intron 2, located between the conserved regions at the 3′ end of exon 2 and the 5′ end of exon 3. At the population-level, GH1 exhibited low heterozygosity (mean Ho = 0.043 ± 0.023; He = 0.059 ± 0.028). Bayesian clustering analyses identified two distinct genetic clusters, corresponding to North African and bighead catfish, apart from the bighead population in Laos, indicating their distinct genetic origins. Evidence of purifying selection was observed in both species. Phylogenetic analysis indicated the presence of lineage-specific alleles in the GH1 gene. Conclusions: These findings provide valuable insights into GH1 polymorphisms in commercially important catfish species and may help to develop future breeding programs aimed at enhancing aquaculture productivity.