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Large rivers and their estuaries are structurally complex and comprise a diversity of habitats supporting a rich biodiversity. As a result, identifying and monitoring fish communities using traditional methods in such systems may often be logistically challenging. Using the mitochondrial DNA 12S MiFish primers, we performed an eDNA metabarcoding analysis to assess the effect of spatial and environmental factors on the variation of the fish community structure along most of the St. Lawrence River/Estuary/Gulf (Québec Canada), a transect spanning 1300 km across a diversity of habitats from a fluviatile non‐tidal section to a marine environment. A total of 129 species were identified including freshwater and marine species. For the freshwater sectors, eDNA identified 80 species compared with the 85 species previously reported based on conventional sampling. eDNA also revealed similar species diversity and communities in the fluviatile section of the St. Lawrence River. Furthermore, our study improved current knowledge about the brackish and marine sections by describing community transition between freshwater and marine fish communities in association with a drastic shift in environmental conditions observed between the end of the fluvial estuary and the beginning of the middle (brackish) estuary. Altogether, this study exemplifies how eDNA metabarcoding is a powerful tool to document fish community shifts in large temperate lotic ecosystems.

Cavefishes often have modified eyes, from small but otherwise functional, to highly degenerate structures embedded in a connective tissue and covered by skin. Darwin assumed that these animals are ‘wrecks of ancient life’, but several genomic studies suggests they are not ‘ancient’. The most radical dating shift is for populations of a Mexican cavefish, Astyanax mexicanus, that have been recently estimated to be at the most a few tens of thousands years old. Despite having highly degenerate eyes, the eye-specific genes of A. mexicanus have low levels of decay. Other blind cavefishes we have examined so far are even older, but also can be dated to the Pleistocene. Here, we estimated the age of blindness of two additional fish species by the level of decay of eye-specific genes. Many pseudogenes were identified in the amblyopsid Typhlichthys subterraneus, suggesting that blindness evolved a few million years ago. In contrast, the blind cichlid Lamprologus lethops appears to be a new case of very recent and rapid eye regression, which occurred in deep river water, an environment similar to caves. Genome-wide analyses support the hypothesis that blindness in cavefishes is never very ancient, and ranges from the Early Pliocene to Late Pleistocene. Together with the description of hundreds of cavefish species, our results suggest that surface fishes were able to recurrently and rapidly adapt to caves and similar small dark ecosystems but the resulting highly specialized blind species with a limited distribution may be evolutionary dead-ends in a relatively short time.

Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxes functional constraints. Subterranean vertebrates are outstanding models to analyze this process, and gene decay can serve as a readout. We sought to understand some general principles on the extent and tempo of the decay of genes involved in vision, circadian clock, and pigmentation in cavefishes. The analysis of the genomes of two Cuban species belonging to the genus Lucifuga provided evidence for the largest loss of eye-specific genes and nonvisual opsin genes reported so far in cavefishes. Comparisons with a recently evolved cave population of Astyanax mexicanus and three species belonging to the Chinese tetraploid genus Sinocyclocheilus revealed the combined effects of the level of eye regression, time, and genome ploidy on eye-specific gene pseudogenization. The limited extent of gene decay in all these cavefishes and the very small number of loss-of-function mutations per pseudogene suggest that their eye degeneration may not be very ancient, ranging from early to late Pleistocene. This is in sharp contrast with the identification of several vision genes carrying many loss-of-function mutations in ancient fossorial mammals, further suggesting that blind fishes cannot thrive more than a few million years in cave ecosystems.

Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxing functional constraints. Gene decay can serve as a read-out of this evolutionary process. Animals living in the dark are outstanding models, in particular cavefishes as hundreds of species evolved independently during very different periods of time in absence of light. Here, we sought to understand some general principals on the extent and tempo of decay of several gene sets in cavefishes. The analysis of the genomes of two Cuban species belonging to the genusLucifugaprovides evidence for the most massive loss of eye genes reported so far in cavefishes. Comparisons with a recently-evolved cave population ofAstyanax mexicanusand three species belonging to the tetraploid Chinese genusSinocyclocheilusrevealed the combined effects of the level of eye regression, time and genome ploidy on the number of eye pseudogenes. In sharp contrast, most circadian clock and pigmentation genes appeared under strong selection. In cavefishes for which complete genomes are available, the limited extent of eye gene decay and the very small number of loss of function (LoF) mutations per pseudogene suggest that eye degeneration is never very ancient, ranging from early to late Pleistocene. This is in sharp contrast with the identification of several eye pseudogenes carrying many LoF mutations in ancient fossorial mammals. Our analyses support the hypothesis that blind fishes cannot thrive more than a few millions of years in cave ecosystems.

Caribbean coral reefs are biodiversity-rich habitats which provide numerous ecosystem services with both ecological and economical values, but nowadays they are severely degraded. In particular, populations of the major framework-building coral Orbicella faveolata have declined sharply, and therefore, understanding how these threatened coral populations are interconnected and how demographic changes have impacted their genetic diversity is essential for their management and conservation. Previous population genetic surveys showed that gene flow in this species is sometimes locally restricted in the Caribbean; however, little genetic data are available for Cuban populations. Here, we analyzed the variation at the mitochondrial DNA control region and six microsatellite loci from O. faveolata colonies from five distant localities representing most of the main coral reefs around Cuba. Both genetic markers showed evidence of genetic differentiation between the northwestern area (Colorados Archipelago) and the other reefs. Colonies from the Colorados Archipelago harbored the largest number of unique mtDNA haplotypes and microsatellite alleles, which suggests long-term large population size or gene flow from other areas of the Caribbean. These results indicate that the Colorados Archipelago area is particularly important for O. faveolata populations and it is well suited for reef management and restoration efforts.

The diversity and ecology of meiofauna in caves is largely unknown. Therefore, we studied one anchialine and five freshwater caves in November 2014 and January 2016 in western Cuba. We recorded 10 invertebrate taxa with the most abundant being: Nematoda, Ostracoda, Acari and Copepoda. The meiofauna communities in the caves were relatively impoverished probably due to the combination of oligotrophic conditions and limited colonization by organisms from outside. We found 28 nematode taxa of which 23 never have been previously reported inhabiting caves. The previously exclusive marine genera Desmodora and Paralongicyatholaimus were reported for the first time in freshwater environments. Ironus cf. ignavus was the most abundant species in agreement with studies elsewhere. In freshwater caves, water runoff and organism dispersal from the surface likely determines the colonization of the sediment. Parthenogenetic and predatory/omnivore nematodes dominated in the studied caves probably due to the physic...

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Pisione is a scaleless group of small scale worms inhabiting sandy bottoms in shallow marine waters. This group was once considered rare, but now 45 described species can be characterized, among others, by their paired, segmental copulatory organs (one to multiple external pairs), which display a complexity of various accessory structures. The evolutionary significance of these unique organs was suggested in the late 1960s, but has been heavily debated since the late 1990s and remains controversial. In the present paper, we study the internal relationships within Pisione, employing combined phylogenetic analyses of both molecular and morphological data from 16 terminals of Pisione, as well as two terminals of Pisionidens, and eight additional scale worms as outgroups. Our taxon sampling covers all geographical areas where the genus has been reported, as well as most of their morphological and copulatory variability, including representatives of the “africana,” “remota,” “crassa,” and “papuensis” groups, established previously by Yamanishi. We hereby provide a first insight into the relationships of the genus, testing previously proposed hypotheses on the evolutionary significance of male copulatory structures within Pisione, while attempting to understand patterns of distribution. The phylogenetic analyses using maximum likelihood and Bayesian methods consistently recovered two large clades spanning the East Atlantic (including the Mediterranean) and the Indo‐Pacific–West Atlantic, respectively. Character optimization on our trees revealed a high degree of homoplasy in both non‐reproductive and sexual characters of Pisione, with buccal acicula found to be the sole apomorphy among the morphological features assessed herein, with none defining the biogeographical subclades within. Overall, our comparative analyses highlight the high degree of morphological variation in this widely distributed genus, rejecting previous assertions of an increasing number and complexity of copulatory structures across the genus.

The main drivers of diversification of freshwater fishes in Cuba are not yet well understood. For example, salt tolerance was thought as the main factor involved in the diversification ofGambusia punctataspecies group in this archipelago. However, evidence from a recent DNA barcoding survey suggested the presence of cryptic species and no correlation between species delimitation and level of salinity. In this study, we analyzed the cryptic diversification ofG. punctataspecies group in Cuba, based on a comprehensive sampling of its distribution and including habitats with different salinity levels. We evaluated the patterns of molecular divergence of the samples by sequencing a set of mitochondrial DNA (mtDNA) regions and genotyping nine nuclear microsatellite loci. We also used cytochrome b gene (cytb) partial sequences and these microsatellite loci to analyze population structure inside putative species. Five mtDNA well-differentiated haplogroups were found, four of them also identified by the analysis of the microsatellite polymorphism which corresponds to two already recognized species,G. punctata, andG. rhizophorae, and three putative new species. The extent of hybrid zones between these groups is also described. In each group, populations inhabiting environments with contrasting salinity levels were identified, indicating a generalized trait not specific toG. rhizophorae. The geographic distribution of the groups suggested a strong association with major relict territories of the Cuban Archipelago that was periodically joined or split-up by changes in seawater levels and land uplifts. Salinity tolerance might have facilitated sporadic and long-distance oversea dispersal but did not prevent speciation in the Cuban archipelago.

Understanding of population genetics is important for the conservation and management of species and ecosystems, providing information on population structure, connectivity, and demography. Here, we review the genetic patterns and processes that shape the natural populations of marine organisms in Cuba, including penaeid shrimps, reef fishes, marine turtles, and bottlenose dolphins. Investigations performed over the last 20 yrs indicate three general patterns of population structure across the Cuban coast: a north-south break, an east-west split in the south, and local genetic differentiation. These patterns have been shaped by factors that include the size of the island, current patterns, lack of suitable habitats for reproduction, larval recruitment, and foraging behaviors. No single trait can predict dispersal and population structure across these diverse groups, but in every case, there are key life-history features that guide connectivity. These include limited larval dispersal in damselfishes and shrimps, social structure in dolphins, and natal homing in marine turtles. Population genetic partitions can reveal the boundaries of isolated ecosystems, guiding the design of marine protected areas.

The genus Rivulus is currently comprised of two species, R. cylindraceus and R. insulaepinorum, which are endemic to Cuba. However, the taxonomic status of the latter species remains dubious because of the poor quality of the original description. In addition, a recent barcoding survey suggests that the two species may be conspecific. The aim of this study was to test the hypothesis that the two species represent a single evolutionary clade. To delimit the species and their evolutionary history, we used a combination of molecular phylogenetic analyses, with both mitochondrial and nuclear sequences, tests of phylogeographic hypotheses, combined with morphological measurements and information on known dispersal barriers and species distribution. None of the data sets support R. insulaepinorum and R. cylindraceus as separate taxa. However, a new species, restricted to the northwestern part of the main island, was identified by phylogenetic analyses, body colour pattern and geographical distribution. The evolutionary distance between the two lineages (cytb, d = 15%; CAM-4, d = 2.5%) indicates a long period of divergence. Phylogeographic analyses shed light on the dispersal history of R. cylindraceus, which probably originated on the Isla de la Juventud. They also suggest that each lineage had contrasting histories; Rivulus sp. is restricted to a relatively small geographic area whereas R. cylindraceus has dispersed considerably and more than once from its centre of origin, probably facilitated by sea level fluctuations. These results strengthen previous findings, i.e. that the diversity of Cuban freshwater fishes is far from well-known and deserves more in-depth studies, and that vicariance and dispersal events have resulted in a complex biogeographical landscape which has had a significant impact on the freshwater fishes of the Caribbean islands.

Connectivity levels among Brazilian reef fish fauna populations have attracted growing interest, mainly between mainland shores and oceanic islands. The Pomacentridae, whose phylogeographic patterns are largely unknown in the Atlantic, are a family of dominant fish in reef regions. We present data on the variability and population structure of damselfishChromis multilineatain different areas along the northeast coast of Brazil and in the waters around the oceanic islands of Fernando de Noronha (FNA) and Saint Peter and Saint Paul Archipelago (SPSPA) through analysis of the HVR1 mtDNA sequence of the control region. The remote SPSPA exhibits the highest level of genetic divergence among populations. Conventional and molecular cytogenetic analysis showed similar karyotype patterns (2n= 48 acrocentrics) between these insular areas. Our estimates reveal three genetically different population groups ofC. multilineataon the Brazilian coast. The level of genetic structure is higher than previous data suggested, indicating complex panel of interactions between the oceanic island and coastal populations of Brazil.

We aimed to identify biotic and abiotic factors underlying genetic structure and diversity of reef fish around Cuba. For three species, Stegastes partitus, Haemulon flavolineatum and Acanthurus tractus, we investigated the effects of shared environmental factors, such as the geography of the Cuban Archipelago, and specific characteristics, such as life history traits, on genetic structure and diversity. Samples were collected at five locations around Cuba. For S. partitus and H. flavolineatum, mitochondrial DNA and microsatellite loci were examined, whereas only mitochondrial DNA polymorphism was analyzed for A. tractus. All three species showed high genetic diversity. Mismatch distribution analyses suggest past population expansion in all species, but at different times in each species. Haplotype network and population genetic analyses suggest that: (1) S. partitus went through a recent population bottleneck in the late Pleistocene, (2) H. flavolineatum went through a population bottleneck but earlier, in the mid-Pleistocene, and (3) A. tractus has had a large and stable population size with coalescence times that go back to the late Pliocene. Genetic polymorphism in H. flavolineatum and A. tractus is homogeneous throughout the archipelago, whereas there is significant genetic structure in S. partitus. Genetic differentiation among S. partitus populations is most likely the result of the combined effects of egg type and oceanic current patterns along the Cuban coast.

Dispersal varies among species according to different biological and environmental factors. It is known that there is strong genetic division between the Ocean Surgeonfish (Acanthurus tractus) and the Barber Surgeonfish (Acanthurus bahianus) in the Caribbean and southern Atlantic biogeographic provinces with relation to the Amazon–Orinoco outflows. We analyzed cytb gene sequence diversity from 149 individuals collected at five localities around Cuba between October 2006 and February 2010. As expected, most individuals had haplotypes identical or closely related to those previously reported for the Caribbean. However, south Atlantic lineage haplotypes were also found in all surveyed localities with frequencies around 5 %. This finding suggests that A. bahianus has dispersed in recent times across the Amazon–Orinoco barrier, probably because environmental perturbations have aided dispersal.

The Cuban gar (Atractosteus tristoechus) is an endemic lepisosteid living in Cuba. Among gars, this species is one of the most threatened and has the smallest natural distribution range. Lepisosteids are air-breathing fishes belonging to the Holostean, a basal non-teleost clade of actinopterygians. Recent studies have indicated that these fishes could be a ‘bridge between tetrapods and teleost biomedical models’. Herein, we sequenced and assembled the first complete mitochondrial genome of A. tristoechus. The total length of the mt genome is 16,290 bp, containing the typical 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a 537 bp length control region.

Despite ongoing efforts to protect species and ecosystems in Cuba, habitat degradation, overuse and introduction of alien species have posed serious challenges to native freshwater fish species. In spite of the accumulated knowledge on the systematics of this freshwater ichthyofauna, recent results suggested that we are far from having a complete picture of the Cuban freshwater fish diversity. It is estimated that 40% of freshwater Cuban fish are endemic; however, this number may be even higher. Partial sequences (652 bp) of the mitochondrial gene COI (cytochrome c oxidase subunit I) were used to barcode 126 individuals, representing 27 taxonomically recognized species in 17 genera and 10 families. Analysis was based on Kimura 2-parameter genetic distances, and for four genera a character-based analysis (population aggregation analysis) was also used. The mean conspecific, congeneric and confamiliar genetic distances were 0.6%, 9.1% and 20.2% respectively. Molecular species identification was in concordance with current taxonomical classification in 96.4% of cases, and based on the neighbour-joining trees, in all but one instance, members of a given genera clustered within the same clade. Within the genus Gambusia, genetic divergence analysis suggests that there may be at least four cryptic species. In contrast, low genetic divergence and a lack of diagnostic sites suggest that Rivulus insulaepinorum may be conspecific with Rivulus cylindraceus. Distance and character-based analysis were completely concordant, suggesting that they complement species identification. Overall, the results evidenced the usefulness of the DNA barcodes for cataloguing Cuban freshwater fish species and for identifying those groups that deserve further taxonomic attention.

Consistent with the limited dispersal capacity of most troglobitic animals, almost all Lucifuga cavefish species have very narrow geographic distribution in Cuba. However, one species, L. dentata, has a wide but disjointed distribution over 300 km in the west of the island. In order to estimate the relative role of vicariance and dispersal in the unexpected L. dentata distribution, we obtained partial sequences of the mitochondrial DNA (mtDNA) cytochrome b (cytb) gene and control region (CR), and then applied Approximate Bayesian Computation (ABC), based on the identification of five genetic and geographic congruent groups of populations. The process that best explains the distribution of genetic diversity in this species is sequential range expansion from east Matanzas to the western Pinar del Río provinces, followed by isolation of groups of populations. We found relative high haplotype diversity and low nucleotide diversity in all but the Havana group, which has high values for both diversity parameters, suggesting that this group has been demographically stable over time. For two groups of populations (Cayuco and Bolondrón), the mismatch distribution analyses suggests past demographic expansion. In the case of the Cayuco region, the star like relationships of haplotypes in the network suggests a recent founding event, congruent with other evidence indicating that this is the most recently colonized region. Over all, the results suggest that a combination of habitat availability, temporal interconnections, and possibly the biological properties of this species, may have enabled its dispersal and range expansion compared to other species of the genus, which are more geographically restricted.

The hamlets are a group of vividly colored fish species of the Serranidae family differentiated only by the color pattern of the body. Although there are divergent views about hamlet taxonomy, experimental and field observations have shown a strong assortative mating, justifying a species status for the different color morphs. Here we analyze the level of evolutionary divergence among six species in respect of mitochondrial DNA, with a view to contrasting the pattern observed with color partitions and previous results obtained with isozymes. The estimated molecular distance among species was low and of the same magnitude as nucleotide diversity within species. Consequently, the net distance and hence the time of divergence between taxa was virtually zero in most comparisons. Although not critically tested, haplotype distribution showed no clear phylogeographic structure,and in many cases the most closely related haplotypes were found at different geographical locations. The absence of differentiated clades between species, based on mitochondrial DNA and isozyme analysis, may have one of two possible origins: a very recent differentiation of species or a lack of absolute barriers to gene flow.However, the available information is insufficient to determine the effect of one or the other, and may require supplementary information from other genes as well as experiments on hybrid fertility. Finally, based on some biological evidence, we suggest that self-fertilization may be an interesting phenomenon to be tested in Hypoplectrus. Published vacas

We investigated the genetic diversity among populations of the shrimp Farfantepenaeus notialis, the most abundant penaeid species around Cuba. A total of 25 allozyme loci were analyzed in samples of shrimps from seven localities at the south central platform of the island (Ana Maria Gulf). Samples from three of these localities and from Batabano Gulf and Guacanayabo Gulf at the south west and south east platforms of the island, respectively, were also characterized at the mtDNA level through sequence variation of a 2027 bp segment including part of the COI and COIII genes. Of the 25 allozyme loci studied 9 were polymorphic: Akp2, Akp3, AmyB, Est3, Gdh, GP7, and Per1, 2 and 3. In contrast to mtDNA, the pattern of allozyme variation among localities revealed strong population structuring at Ana Maria Gulf, with significant F st in all pairwise comparisons. The magnitude of F st estimates as well as the grouping pattern obtained by a UPGMA analysis based on a distance matrix indicated that the level of differentiation was concordant with the geographical position of the localities and the hydrographic regime. Homogeneity of mtDNA suggested that differentiation of allozyme loci might be due to more recent events rather than historical isolation of the sampled populations. Ana Maria and Guacanayabo Gulf populations were differentiated by mtDNA from Batabano Gulf, at the southwestern end of the island. The analysis showed three restriction site differences among them, suggesting genetic isolation of the two regions. The present results also suggest that an artificial introduction of larvae from Tunas de Zaza into Batabano Gulf, in an effort to repopulate this fishing region, may have been ineffective.

The Epinephelidae form a group of species of high biological and economical interests. It´s phylogeographic patterns are not well known especially the distributed populations in the western region of the Atlantic Ocean. Among the representatives is a small species called Cephalopholis fulva, Coney, which presents a wide geographical distribution, polychromia, hermaphroditism and is quickly becoming a large target for the exploration of commercial fishing. The genetic and historical demography were obtained through the partial sequence analysis of Control Region from six locations on the coastline of Brazil from the northeast coast to the southwest coast, including the oceanic islands of Rocas Atoll and Fernando de Noronha Archipelago. The analyzed samples revealed a high genetic variability and a strong gene flow among the sampled locations. Additionally, the genetic data revealed that population expansions probably occurred due to the changes in the sea levels that occurred during the Pleistocene. The large population connectivity found in Coney constitutes relevant conditions for their biological conservation. Epinephelidae forma um grupo de espécies de grande interesse biológico e econômico. Seus padrões filogeográficos são pouco conhecidos, principalmente nas populações distribuídas na região oeste do Oceano Atlântico. Entre seus representantes está a pequena espécie Cephalopholis fulva, Coney, a qual apresenta ampla distribuição geográfica, policromia e hermafroditismo, além de estar se tornando um alvo crescente da exploração pesqueira comercial. Os dados genéticos e histórico-demográficos foram obtidos através da análise de sequências parciais da Região Controle de seis localidades do litoral brasileiro, desde o Nordeste até o Sudeste do Brasil, incluindo as ilhas oceânicas do Atol das Rocas e do arquipélago Fernando de Noronha. As amostras analisadas revelaram uma alta variabilidade genética e um forte fluxo gênico entre as localidades amostradas. Além disso, os dados genéticos relevaram expansões populacionais provavelmente relacionadas às mudanças no nível do mar ocorridas durante o Pleistoceno. A ampla conectividade populacional presente em Coney constitui uma condição relevante para a sua conservação biológica.

Abstract Part of the mitochondrial 16S-ribosomal RNA gene (around 400 nucleotides) of Penaeus notialis and Penaeus schmitti has been amplified and sequenced. The comparison of sequences reveals an 11% nucleotide divergence between the two species. When compared with that of the homologous fragment in Artemia salina and Drosophila yakuba, the secondary structure appears well conserved in spite of high nucleotide divergence due to numerous substitutions and additions/deletions. Sequences have been obtained for six individuals of P. notialis belonging to the same population, their comparison shows a 0.7% nucleotide diversity.

We analyzed the spatiotemporal genetic structure of Farfantepenaeus notialis populations using five microsatellites loci in order to understand the influence of natural events such as hurricanes on the genetic drift/migration balance as the main cause for the variation of allele frequencies over time. The results were compared with the previous ones obtained from allozymes and mtDNA. High and stable genetic diversity levels (He = 0.879 ± 0.0015) were found over eight years for the populations that inhabit the south Cuban platform, however significant changes of allele frequencies were detected over time. The F ST estimates, albeit low, revealed significant differences among populations inside the Ana Maria Gulf for 1995 but not for the 1999 and 2003 samples. The F ST, AMOVA and the genetic distance analysis revealed the instability of the genetic structure over time in accordance with allozymes results. The correspondence of the microsatellite results with those obtained from allozymes confirm the effects of migration enhanced by natural events as the main cause of the temporal variation of allele frequencies. The genetic drift effect was discarded through the evaluation of Ne and the M ratio, while natural selection effects were rejected because of the lowest probability of microsatellite loci being under selective pressures. The microsatellite data are also consistent with the results obtained with mtDNA in detecting significant and persistent genetic differences between the Gulfs of Ana Maria and Batabano for the years 1995 and 2003.

Population genetic studies carried out on penaeid shrimps have disclosed different patterns of population subdivision, revealing new aspects of shrimp biology as well as the effects of historical contingency molding those patterns. However, the stability of observed allele frequencies over time still remains untested. The objective of this article is to show the analysis of the temporal variation of allozymes in a shrimp species inhabiting Cuba which proves that the genetic structure of this species could significantly change in time. The study involves four populations of Farfantepenaeus notialis sampled in a period of 8 years. The significant statistics obtained from partitions observed in 1995 were not detected in 2003 (as suggested by AMOVA and F ST ), whereas temporal genetic differentiation and heterozygosity became highly significant. The results strongly suggest that the effect of migrations could be the cause for the loss of F. notialis genetic structure in 2003. It is therefore imperative to call attention on the vulnerability of these populations when facing unstable environmental and habitat conditions.

Complete sequences of seven protein coding genes from Penaeus notialis mitochondrial DNA were compared in base composition and codon usage with homologous genes from Artemia franciscana and four insects. The crustacean genes are significantly less A + T-rich than their counterpart in insects and the pattern of codon usage (ratio of G + C-rich versus A + T-rich codon) is less biased. A phylogenetic analysis using amino acid sequences of the seven corresponding polypeptides supports a sister-taxon status for mollusks–annelid and arthropods. Furthermore, a distance matrix-based tree and two most-parsimonious trees both suggest that crustaceans are paraphyletic with respect to insects. This is also supported by the inclusion of Panulirus argus COII (complete) and COI and COIII (partial) sequence data. From analysis of single and combined genes to infer phylogenies, it is observed that obtained from single genes are not well supported in most topologies cases and notably differ from that of the tree based on all seven genes.

Farfantepenaeus notialis is an important resource for fisheries in Cuba. For this reason and for a sustainable exploitation it is important to study their population structure and genetic variability. We report and characterize microsatellites as genetic markers from this species. Fifteen microsatellite polymerase chain reaction (PCR) primers were designed and tested in some individuals from different populations. Seven pair of primers showed reliable amplification products and five were polymorphic. The allele number ranged from 4 to 33, and the observed and expected heterozygosities were relatively high with values between 0.63 and 0.74 and 0.56 and 0.81, respectively. Departures from Hardy–Weinberg equilibrium were observed for all loci.