Dr. Waldir Berbel-Filho

We present the first genome assembly of Psalidodon fasciatus , a rheophilic fish recently classified within Acestrorhamphidae and distributed across major South American river basins. Known for its karyotypic diversity and cryptic speciation potential, P. fasciatus was sequenced using Illumina Hi-Seq and assembled with SPAdes and Zanfona, resulting in 471,706 scaffolds at 60× coverage. The assembled genome is available in GenBank (Assembly ID: ASM5207532v1) and provides a valuable resource for evolutionary and taxonomic studies in Brazilian ichthyofauna.

The Cynodonichthys tenuis species group has one of the largest distribution ranges among the Central American rivulids, ranging from the Atlantic slope of southeastern Mexico to Colombia. The enigmatic species Cynodonichthys myersi was described by Hubbs in 1936 from Yucatan. Since then, no further collection of C. myersi specimen has been reported. C. myersi was later considered only a junior synonym of C. tenuis. Here, we report the rediscovery of C. myersi in northern Yucatán mangroves and validate its status as a distinct species through morphological and molecular analyses. The average cytochrome oxidase 1 (cox1) genetic distance between C. myersi and other species from C. tenuis group samples was 8.7%. Our phylogenetic analysis revealed that C. myersi is more closely related to Cynodonichthys species distributed in Panama (Cynodonichthys brunneus, Cynodonichthys weberi, Cynodonichthys montium by ~1700 km distant) than to C. tenuis contradicting expectations based on geographic proximity, suggesting independent ancestral dispersal routes between C. myersi and C. tenuis in Mexico. C. myersi can be differentiated by distinct colouration patterns: males exhibit dark spots over the anal fins on iridescent greenish blue (cyan), whereas females display a spotted pattern in caudal fin. The fish were found at the soil-water interface and out of water, revealing a potential amphibious behaviour.

Asexual species, despite lacking recombination, can evolve in response to environmental changes and influence the evolutionary trajectory of coexisting sexual species. Gynogenesis, where asexual females rely on sperm from males of a different species, offers a unique perspective on the eco-evolutionary dynamics between asexual females and their sexual hosts. The Amazon molly,
, is a gynogenetic species that primarily uses sperm from two sympatric sexual species: the sailfin molly (
) and the Atlantic molly (
). To understand shape variation in an asexual species relative to their sexual hosts, we analysed shape variation among wild Amazon mollies and their sexual hosts. We tested three hypotheses: (i) Amazon mollies mimic their sexual hosts to enhance mating opportunities (sexual mimicry hypothesis); (ii) ecological interactions or male mate choice drive morphological divergence (character displacement hypothesis); and (iii) Amazon mollies exhibit random shape variation due to their asexual nature (null hypothesis). Our findings revealed significant shape variation in Amazon mollies, which differ from their sexual hosts in a host-specific manner (e.g. Amazon mollies with
resemble
and vice versa), supporting character displacement at the interspecific level in a sexual-asexual system.

Listrura and Microcambeva are two genera of small, rare and elusive catfishes of the Trichomycteridae family, endemic to the Atlantic Forest coastal drainages in Brazil. Listrura comprises 13 species with slender bodies, absent pelvic fins, and a distinct caudal-fin and caudal-peduncle morphology, while Microcambeva includes eight species with translucent bodies, typically buried in sandy substrates with exposed nasal barbels. The two genera inhabit fragile environments that are undergoing accelerated degradation, with Listrura camposae and L. nematopteryx classified as “Critically Endangered” (CR), and L. picinguabae as “Near Threatened” (NT). Microcambeva species face similar threats, with M. bendego proposed as CR and M. draco as “Endangered” (EN). Over the past two decades, collection efforts and taxonomic descriptions have expanded the diversity of these two genera, with descriptions of 11 species of Listrura and seven of Microcambeva species in that period. Recently, Costa & Katz (2021) further subdivided each genus into three subgenera based on pectoral-fin morphology and molecular phylogenetic results. To address gaps in genetic data for those taxa, we herein present whole-genome sequences for three Listrura species — L. nematopteryx , L. tetraradiata , and L. boticario — and five Microcambeva species — M. barbata , M. watu , M. jucuensis , M. bendego , and M. ribeirae . These genomic data are critical for future studies on the evolutionary history and systematics of these unique catfishes, contributing to foundational knowledge of their biodiversity.

The role of hybridization as a formative process in evolution has received much attention in the past few decades. A particularly fascinating outcome of hybrid speciation is the formation of asexual hybrid species. The Amazon molly (Poecilia formosa) is such a hybrid and originated from a P. mexicana mother and a P. latipinna father. Consequently, a heterospecific mating must have occurred leading to the Amazon molly, indicating a breakdown of any potential prezygotic isolation between parental species. Here we studied the female mate preferences of extant P. mexicana and P. latipinna from several populations using standard binary choice tests with males of both sexual species that were matched for size. Poecilia mexicana and P. latipinna can be crossed in the lab, however, the offspring are not asexual, but sexual F(1)s. In our study, we generated F(1)s and tested their mating preferences with sexual males of both P. mexicana and P. latipinna against F-1 males. Overall, our results show that in extant P. mexicana and P. latipinna no female preference for conspecific males was detectable. Consequently, heterospecific matings are possible and not hindered by any apparent behavioral prezygotic isolation. If female preferences in these species were comparable around the time the Amazon molly originated as a hybrid species ca. 100,000 years ago, matings leading to hybrids would be very likely. F-1 females also have no discernable mating preferences for either sexual males or F-1 males. Such lack of prezygotic behavioral isolation could potentially lead to F-2 individuals, backcrosses, and introgression.

Widespread species often experience significant environmental clines over the area they naturally occupy. We investigated a widespread livebearing fish, the Sailfin molly (Poecilia latipinna) combining genetic, life-history, and environmental data, asking how structured populations are. Sailfin mollies can be found in coastal freshwater and brackish habitats from roughly Tampico, Veracruz in Mexico to Wilmington, North Carolina, in the USA. In addition, they are found inland on the Florida peninsula. Using microsatellite DNA, we genotyped 168 individuals from 18 populations covering most of the natural range of the Sailfin molly. We further determined standard life-history parameters for both males and females for these populations. Finally, we measured biotic and abiotic parameters in the field. We found six distinct genetic clusters based on microsatellite data, with very strong indication of isolation by distance. However, we also found significant numbers of migrants between adjacent populations. Despite genetic structuring we did not find evidence of cryptic speciation. The genetic clusters and the migration patterns do not match paleodrainages. Life histories vary between populations but not in a way that is easy to interpret. We suggest a role of humans in migration in the sailfin molly, for example in the form of a ship channel that connects southern Texas with Louisiana which might be a conduit for fish migration.

Non-genetic sources of phenotypic variation, such as the epigenome and the microbiome, could be important contributors to adaptive variation for species with low genetic diversity. However, little is known about the complex interaction between these factors and the genetic diversity of the host, particularly in wild populations. Here, we examine the skin microbiome composition of two closely-related mangrove killifish species with different mating systems (self-fertilising and outcrossing) under sympatric and allopatric conditions. This allows us to partition the influence of the genotype and the environment on their microbiome and (previously described) epigenetic profiles. We find the diversity and community composition of the skin microbiome are strongly shaped by the environment and, to a lesser extent, by species-specific influences. Heterozygosity and microbiome alpha diversity, but not epigenetic variation, are associated with the fluctuating asymmetry of traits related to performance (vision) and behaviour (aggression). Our study identifies that a proportion of the epigenetic diversity and microbiome differentiation is unrelated to genetic variation, and we find evidence for an associative relationship between microbiome and epigenetic diversity in these wild populations. This suggests that both mechanisms could potentially contribute to variation in species with low genetic diversity.
Species with low genetic diversity have limited capacity to adapt to environmental change. This study finds that the skin microbiome and non-genetic (epigenetic) modifications of the DNA represent additional sources of variation that could help low diversity fish survive environmental challenges.

The Mexican Rivulus, Millerichthys robustus , is an enigmatic species of seasonal killifish endemic of the Southeast Mexico that has changed paradigms on the evolution of annualism in killifishes. This species survives in ephemeral environments that experience a period of seasonal drought that causes the death of all adult fish. However, populations persist due to their drought-resistant embryos capable of arresting their development in diapause until the next the rainy season. Millerichthys evolved unique characteristics within annual killifishes as a functional sequential hermaphroditism, in which females change to males (protogynous) under perceived conditions of mate competition. Also, M. robustus express different color phenotypes in both sexes: five-color phenotypes continuously distributed in various perceptual units between yellow and red in males, and different number of ocelli disposed in caudal peduncle in females. The phylogenetic relationships of M. robustus revealed that it is a sister clade to two non-annual species found exclusively in Cuba ( Rivulus cylindraceus and Rivulus berovidesi ), indicating that the annual life cycle, through the acquisition of embryonic diapause, has evolved independently in this species. Here, we present the complete genome sequences for the North American annual killifish Millerichthys robustus . The raw data and assembled genome are available in GeneBank.

Asexual reproduction is ancestral in prokaryotes; the switch to sexuality in eukaryotes is one of the major transitions in the history of life. The study of the maintenance of sex in eukaryotes has raised considerable interest for decades and is still one of evolutionary biology's most prominent question. The observation that many asexual species are of hybrid origin has led some to propose that asexuality in hybrids results from sexual processes being disturbed because of incompatibilities between the two parental species' genomes. However, in some cases, failure to produce asexual F1s in the lab may indicate that this mechanism is not the only road to asexuality in hybrid species. Here, we present a mathematical model and propose an alternative, adaptive route for the evolution of asexuality from previously sexual hybrids. Under some reproductive alterations, we show that asexuality can evolve to rescue hybrids' reproduction. Importantly, we highlight that when incompatibilities only affect the fusion of sperm and egg's genomes, the two traits that characterize asexuality, namely unreduced meiosis and the initiation of embryogenesis without the incorporation of the sperm's pronucleus, can evolve separately, greatly facilitating the overall evolutionary route. Taken together, our results provide an alternative, potentially complementary explanation for the link between asexuality and hybridization.

Hybridization is a natural process whereby two diverging evolutionary lineages reproduce and create offspring of mixed ancestry. Differences in mating systems (e.g., self-fertilization and outcrossing) are expected to affect the direction and extent of hybridization and introgression in hybrid zones. Among other factors, selfers and outcrossers are expected to differ in their mutation loads. This has been studied both theoretically and empirically; however, conflicting predictions have been made on the effects mutation loads of parental species with different mating systems can have on the genomic composition of hybrids. Here, we develop a multi-locus, selective model to study how the different mutation load built up in selfers and outcrossers as a result of selective interference and homozygosity impact the long-term genetic composition of hybrid populations. Notably, our results emphasize that genes from the parental population with lesser mutation load get rapidly overrepresented in hybrid genomes, regardless of the hybrids own mating system. When recombination tends to be more important than mutation, outcrossers' genomes tend to be of higher quality and prevail. When recombination rates are low, however, selfers' genomes may reach higher quality than outcrossers' genomes and prevail in the hybrids. Taken together, these results provide concrete insights into one of the multiple factors influencing hybrid genome ancestry and introgression patterns in hybrid zones containing species with different mating systems.