Objective: The Common Snook Centropomus undecimalis is a species widely distributed throughout the western Atlantic, playing a key ecological role in coastal and estuarine ecosystems. Despite its broad distribution from Florida to southeastern Brazil, little is known about the genetic patterns underlying its population connectivity. This study aimed to characterize the genetic structure of this species and to infer patterns of genetic diversity and connectivity across its range. Methods: A total of 100 individuals collected from Florida to southeastern Brazil were genotyped at 11 microsatellite loci. Genetic structure was assessed using Bayesian clustering analysis, discriminant analysis of principal components, and analysis of molecular variance. Genetic differentiation among populations was estimated by pairwise F-ST, and recent gene flow was inferred from migration proportions among the identified genetic profiles. Results: Three distinct genetic profiles were identified: one exclusive to the southern Gulf of Mexico (Gulf Profile) and two along the Atlantic coast (Northern and Southern profiles), both contributing to a central mixed zone in northern South America. Analysis of molecular variance revealed greater variation within populations (68.8%). When admixed individuals (<80% assignment) were excluded, the variation among groups increased to 27.2%, while within-group variation remained high (68.4%). The Gulf Profile showed strong differentiation from the others (F-ST = 0.33-0.39), whereas differentiation between the Northern and Southern profiles was lower but significant (F-ST = 0.038). Recent migration analysis indicated high genetic self-recruitment within each profile (68-99%) and limited gene flow among them, except for significant migration from the Southern Profile to the Northern Profile (migration rate = 0.301). Genetic diversity was high across all profiles, with greater allelic richness and heterozygosity in the Gulf Profile and lower values in the Southern Profile; 90 private alleles were identified, most of them in the Gulf Profile. Conclusions: The Common Snook exhibits an isolated stock in the southern Gulf of Mexico, likely maintained by historical processes and local oceanographic dynamics, such as the Loop Current and cyclonic vortices. Along the Atlantic coast, two distinct genetic profiles (Northern and Southern) are connected by a transitional zone in northern South America characterized by extensive genetic admixture. Atlantic connectivity appears to be facilitated by ocean currents and the species' broad ecological plasticity, including tolerance to salinity variation and diadromous migrations. These findings provide valuable insights for conservation and fisheries management strategies throughout the distributional range of this species.

AbstractThis study aims to enhance our understanding of the temporal and spatial processes scales governing the evolutionary diversification of Neotropical birds with Trans‐ and Cis‐Andean populations of the species Attila spadiceus from South and Central America. Through a multilocus analysis of the mitochondrial (CytB and ND2) and nuclear genes (I7BF, I5BF, and G3PDH) of 41 samples representing six subspecies, we describe the existing molecular lineages of A. spadiceus, and estimate their demographic dynamics. We used Ecological Niche Modeling (ENM) with six different algorithms to predict the potential distribution of A. spadiceus in both present‐day and past scenarios, examining the overlap climatic niche between Cis‐ and Trans‐Andean lineages. The analysis confirms a relatively recent divergence of the Trans‐ and Cis‐Andean lineages, at approximately 0.25 million years ago (Ma). The niche modeling supports the existence of a dynamic scenario of the expansion and retraction of forest corridors in northwestern South America during the last glaciation. This suggests that the earlier orogenesis of the Andes was not a primary determinant of this dichotomy. Additionally, the analysis of population dynamics indicated a trend of increasing population size starting at 0.05 Ma for both lineages. Our findings highlight the significance of Pleistocene Forest corridors north of the Andes as the key factor maintaining communication before the separation of the lineages, likely associated with the retraction of this forest. We highlight the absence of any significant differentiation between the disjunct Amazonian and Atlantic Forest populations, at both part of the Cis‐Andean lineage. The phylogeographic profile of A. spadiceus diverges from the patterns observed in other Neotropical birds, which emphasizes the need for further research on the role of the forest corridors of the northern Andes as drivers of diversification, to provide comprehensive insights into the processes that led to the formation of the region's present‐day avian diversity.

The snooks (Centropomus spp.) are a group of 13 morphologically similar fish species that are widely distributed off the Atlantic and Pacific coasts of the Americas. This study used a multilocus approach to assess the evolutionary relationships within the genus, and to estimate the divergence times of all the taxa. A total of 105 specimens were analyzed throughout the geographic distribution of the different species. The results of the analyses suggest that the genus Centropomus is composed of four species groups, which originated in the Miocene (~20 Ma) with the common ancestor of the genus probably inhabiting coastal environments in the Americas prior to its diversification. However, most of the cladogenetic events that determined the extant diversity of the genus occurred more recently, during the Pliocene-Pleistocene transition. The samples analyzed here permitted identify three distinct clades within the C. parallelus/C. mexicanus complex, with Centropomus mexicanus likely being restricted to the Gulf of Mexico. The results of the present study also corroborated the existence of two distinct lineages in Centropomus parallelus and identified two previously undescribed lineages in Centropomus viridis. The estimates of divergence times indicated that the formation of the Isthmus of Panama played an important factor in the evolution of the snooks, as weel as oscillations in sea level and ecological adaptations. The type of habitat is related to the evolutionary history of the genus, with the ancestral forms likely inhabiting riverine shoreline environments. Our findings highlight the importance of spatially comprehensive sampling for a better understanding of the evolutionary history of the centropomids, and reinforce the need for a more comprehensive taxonomic review of the genus Centropomus.

Birds are the vertebrate group most used in studies that attempts to decipher the events that have molded the diversification of the Amazonian biota. However, inconsistencies related to the existence of polytypic species, associated with the limited samples available for many regions, hamper the accurate reconstruction of phylogeographic patterns. In particular, no molecular study has yet included all the subspecific taxa currently recognized in the Band-tailed Manakin, Pipra fasciicauda . This species encompasses a complex of subspecies differentiated by their morphological traits and distinct regional distributions. The present study investigated the current taxonomic and phylogeographic configuration of P. fasciicauda using a multilocus molecular approach to decipher the biogeographic events that determined the diversification of this group. This analysis included all the recognized subspecies, sampled widely throughout their respective areas of occurrence. The molecular data indicate the existence of three monophyletic lineages that coincide only partially with the current subspecific classification of the group. Lineage 1 grouped all the specimens of the subspecies Pipra fasciicauda purusiana and Pipra fasciicauda saturata . Lineage 2 was composed of the individuals of Pipra fasciicauda fasciicauda and Pipra fasciicauda calamae , while lineage 3 was formed by the specimens of Pipra fasciicauda scarlatina . Lineage 1 was estimated to have diverged from the other lineages by around 0.43 Mya, while lineages 2 and 3 would have separated by 0.17 Mya, which indicates that their current phylogeographic configuration was determined by events occurring during the middle Pleistocene. The demographic analyses revealed a process of recent geographic expansion, with dispersal events molding the gene flow among lineages. As observed in other bird taxa, the diversification of P. fasciicauda has been associated with the hydrographic dynamics of the Amazon basin, together with climatic shifts, which have combined to determine the differentiation of the populations from west to east within the basin.

Investigating parallel roles of geography and environmental heterogeneity in diversification provides insights on how neutral and selective forces drive evolution of biological systems. Here, we investigate whether geographic and climatic distances explain either genetic or phenotypic variation in Blue-crowned Manakins ( Lepidothrix coronata ), a polychromatic bird species that is broadly distributed in the Neotropics. We tested the hypotheses of isolation by distance and environment through an integrative approach using genetic, colorimetric, geographic, and environmental data. Through structural equation modeling and multiple matrix regression with randomization statistics, we tested whether intraspecific genetic or phenotypic (plumage color) diversity is associated with variation in geographic and environmental distances among localities. Genetic and color diversity were not correlated: color variation was marginally associated with latitude; and genetic distances were explained by linear and least-cost geographic distances, conforming to predictions of isolation by distance and by environment. We suggest a combined effect of genetic drift and environmental heterogeneity in driving the genetic diversification at the regional scale, and adaptation to local environments operating in the diversification of adult male plumage coloration.

The Amazonian snook ( Centropomus irae ) is the most recently described fish species of the genus Centropomus , which is endemic to the marine biogeographic region known as the Amazon River Plume, on the northern coast of Brazil. In the present study, we evaluated the population genetics, phylogeography, and evolutionary history of this species based on sequences of the Control Region of the mitochondrial genome. We analyzed a total of 87 specimens, including 39 C. irae and 48 specimens of the sister species Centropomus undecimalis , from the coast of the western South Atlantic. The results of the study revealed high levels of genetic diversity in both species, with no evidence of any genetic differentiation among the localities sampled for either species. This may be related to the typical migratory and reproductive behavior of the snooks. The analyses of the demographic history of the species identified a discrete process of population expansion in C. undecimalis at around 20,000 years ago, whereas C. irae passed through a marked population expansion approximately 30,000 years ago, which was probably linked to the formation of the Amazon plume and the fluctuations in sea levels that occurred during the late Pleistocene.

Populations peripheral to a species’ distribution are more susceptible to new selective pressures, changes, differentiation, and extinction. The Sooty Swift Cypseloides fumigatus (Apodidae) is a rare bird found mainly in central and southeastern South America. Populations of this species are resident in some localities throughout the year, whereas other populations migrate following the breeding season. Recently, a northern population was found well beyond the limits of its known distribution, with approximately 1000 km of occurrence gap between this newly discovered population and the southern distribution. Here, we reveal changes in species distribution over time, as well as compare the morphometric and genetic patterns of populations in the central-southern distribution of the Atlantic Forest and the northern peripheral population within the Caatinga. Our climate niche models indicate a scenario of expanding species distribution during the Last Glacial Maximum, which potentially drove the colonization of the northernmost population. This scenario of peripheral isolation is also supported by the spatial morphometric and genetic variation among populations of the humid forest enclave within the Caatinga and the Cerrado–Atlantic Forest populations. These findings provide important insights into the connectivity between distant Sooty Swift populations, the species' migratory behavior, as well as implications for conservation.

The Cerrado encompasses a complex network of hydrographic basins, which is responsible for the formation and maintenance of the riparian and gallery forests. Alterations in the vegetation resulting from the paleoclimatic changes that occurred during the Pleistocene influenced the current distribution of these humid forests. To understand of the evolutionary dynamics of this landscape on the population structure of the associated organisms, we studied the population genetics of the Antilophia galeata (Pipridae), a bird endemic to the gallery forests of the Cerrado. For this, we evaluated the variability of the mitochondrial control region of 71 A. galeata specimens from 18 localities distributed throughout the Cerrado. The results indicated the existence of significant substructure among the populations located in the peripheral areas of the Cerrado, in comparison with the populations found in the central portion, reflecting historical changes in the environment. We also found high levels of diversity in all the populations, while the analysis of the demographic history revealed a scenario of stability. Overall, then, these findings indicate that the historical modifications of the gallery forest distribution may have been most accentuated in the peripheral zones, with a greater stability and connectivity persisting in the central portion of the biome.

Genetic information is still underestimated in conservation policies, seldom being monitored or included in management strategies. Monitoring changes in genetic diversity over time in endangered species is useful to anticipate possible risks associated with reduced genetic variation. The Araripe Manakin (Antilophia bokermanni) is a Critically Endangered species, probably with a historically low level of genetic diversity and currently facing demographic population decline. This is the first study to present a fine-scale spatio-temporal genetic monitoring for the Araripe Manakin. Using microsatellite loci, genotyped at two time periods (2003–2004 and 2015–2017), we conclude that genetic diversity has been relatively stable in this short-term assessment, with limited signs of population structure between time frames, and no current population structure within past or present species distribution. However, we also detect signs of genetic bottleneck and evidence that suggest that mating is not presently random. Our results corroborate that the species is a resilient bird, but habitat loss and degradation are jeopardizing Araripe Manakin’s persistence. The species comprises a unique small population, and restoration of habitat quality and connectivity should continue to maintain its viability. Nonetheless, given the low genetic diversity observed, we further identify some challenges and recommend solutions for the implementation of genetic information in the current conservation effort of the Araripe Manakin.

Abstract: Few twinning events have been recorded in the West Indian manatee (Trichechus manatus, Sirenia: Trichechidae) and no previous published study has provided confirmation of this phenomenon based in molecular tools. Here we investigate a possible case of twinning in an endangered Brazilian population of T. manatus using molecular tools. We analyzed two male neonates found stranded in Ceará State, on the northeastern coast of Brazil. The DNA of both individuals was isolated, and 10 microsatellite loci were amplified and genotyped. Following the identification of the alleles, the probabilities of identity by descent (∆7 and ∆8) and relatedness (rxy) were calculated using estimators that evaluate inbreeding. The two individuals shared most of the alleles, with differences in the genotypes being identified in only two loci. All the estimators identified a level of relatedness compatible with that found between siblings (selfed or outbred), indicating they were dizygotic twins. This is the first confirmed case of fraternal twins in free-ranging West Indian manatees in South America. The recognition of this type of twinning provides elements to improve actions for the rehabilitation of stranded animals and their subsequent release to the environment.

For the epic journey of autumn migration, long-distance migratory birds use innate and learned information and follow strict schedules imposed by genetic and epigenetic mechanisms, the details of which remain largely unknown. In addition, bird migration requires integrated action of different multisensory systems for learning and memory, and the hippocampus appears to be the integration center for this task. In previous studies we found that contrasting long-distance migratory flights differentially affected the morphological complexity of two types of hippocampus astrocytes. Recently, a significant association was found between the latitude of the reproductive site and the size of the ADCYAP1 allele in long distance migratory birds. We tested for correlations between astrocyte morphological complexity, migratory distances, and size of the ADCYAP1 allele in three long-distance migrant species of shorebird and one non-migrant. Significant differences among species were found in the number and morphological complexity of the astrocytes, as well as in the size of the microsatellites of the ADCYAP1 gene. We found significant associations between the size of the ADCYAP1 microsatellites, the migratory distances, and the degree of morphological complexity of the astrocytes. We suggest that associations between astrocyte number and morphological complexity, ADCYAP1 microsatellite size, and migratory behavior may be part of the adaptive response to the migratory process of shorebirds.

The mitochondrial cytochrome oxidase c subunit 1 (COI) gene has been widely used in phylogenetic studies of crustaceans and analyses in population genetics. As COI studies have become more popular, there has been an increase in the number of reports of the presence of nuclear insertions of mitochondrial DNA (Numts) and mitochondrial heteroplasmy. Here, we provide evidence of both types of event in the COI sequences of Macrobrachium amazonicum, an economically important freshwater prawn, which is widespread in South America. Heteroplasmy and Numts were confirmed by different methods of DNA extraction (genomic, mitochondrial, and nuclear-enriched DNA), cloning, and sequencing, and were observed in 11 of the 14 populations sampled, primarily in the Amazon region. We discuss how the occurrence of these events affects the interpretation of the genetic relationships among the M. amazonicum populations, and we recommend caution when using COI for genetic inferences in prawns of the genus Macrobrachium, and in particular that any analysis should include nuclear markers.

Aim Neotropical savanna birds occur north and south of, but mostly not in the Amazon Basin, except for a few isolated savanna patches. Here, we investigate the phylogeography of 23 taxa of Neotropical savanna birds co-distributed across multiple isolated savanna patches to assess to what extent these species have a shared history of spatial diversification. We explore the role of the forested Amazon Basin as a vicariant barrier separating northern and southern populations, particularly focusing on the role of the coastal savannas of Amapa as a potential corridor of gene flow between northern and southern populations. Location Neotropical savannas. Taxon Aves. Method We employ 775 mtDNA samples of 24 co-distributed savanna bird taxa from all major savanna patches in South America to infer phylogeographic patterns. For this purpose, we use 24 genomic samples (UCEs) of a subset of 12 taxa in addition to the mtDNA samples to estimate timing of divergence across the Amazon Basin. We use phylogeographic concordance factors (PCF) to assess the level of phylogeographic congruence across co-distributed taxa. Finally, we assess to which level physical distance drives genetic structuring by estimating isolation-by-distance (IBD) effects. Results We find that although the study taxa generally do not share similar diversification patterns geographically, many have at least two distinct genetic groups, one north and one south of the Amazon Basin, that have only recently diverged. The timing of divergence between both areas is generally centered in the late Pleistocene, but somewhat variable, indicating there is no single vicariant event responsible for driving diversification. Main conclusions Variability in divergence times indicates that landscape processes have not led to shared phylogeographic responses, which indicates a relatively minor role for vicariance. Shallow divergences suggest that Neotropical grassland habitats may have recently been more connected or that gene flow has played an important role. We did not find evidence of a single dominant corridor of dispersal between savannas north and south of the forested Amazon Basin.

The present study aimed to confirm the occurrence of a hybridization event between the band-tailed manakin (Pipra fasciicauda) and the crimson-hooded manakin (Pipra aureola), based on the existence of a specimen that presents morphological traits of both taxa. We analyzed 297 taxidermized skins of adult males of the two species, including the potential hybrid. We also analyzed the mitochondrial (ND2, ND3 e COI) and nuclear (FGB-I5, MB-I2 e GAPDH-I3) genes of 12 adult specimens of the two taxa, diagnosed phenotypically, in addition to the potential hybrid. The analyses of the plumage indicated that the potential hybrid has an intermediate pattern of white banding on the tail that is less extensive than that found in Pipra fasciicauda, but that its other phenotypic traits are characteristic of Pipra aureola. The molecular topologies revealed two clades, one that groups P. aureola together with the potential hybrid, and the other that corresponds to P. fasciicauda. These findings allowed us to confirm the occurrence of a process of hybridization and potential introgression through secondary events in the P. aureola lineage.

The Serra Spanish Mackerel, Scomberomorus brasiliensis is one of the principal fishery resources found in the tropical and subtropical waters of the western South Atlantic. Declining catches of S. brasiliensis off the coast of northeastern Brazil indicate that this species is being overfished. Despite the importance of this species to local fisheries, few data are available on its genetic diversity or population parameters. Given this scenario, the present study evaluated the genetic variability of S. brasiliensis off the coast of the western South Atlantic, based on mitochondrial genes. We compiled two databases, one with partial sequences of the MT-CYB gene (N = 105), and the other of the MT-ND4 gene of the Serra Spanish Mackerel, sampled from eight localities, ranging from Cumana in Venezuela to Paranaguá, in southern Brazil. The results of the analysis indicate low levels of genetic diversity in the study. Samples from Cumana, on the coast of Venezuela were the most differentiated, although the results of the AMOVA were not significant. The PhiST values, the genetic divergence, and the haplotype network all indicate the widespread sharing of haplotypes by the mackerel from all the different localities. Analyses of the historical demography, based on both markers, indicate the occurrence of past population expansion, coinciding with fluctuations in sea level that occurred 10,000 years ago. The demographic and phylogeographic analyses of the mitochondrial DNA revealed the existence of a single genetic stock of S. brasiliensis on the coast of the western South Atlantic according to. These findings are fundamental to the development of effective conservation strategies.

Arapaima is a widely-distributed fish of enormous economic importance in the Amazon region. In the present study, a total of 232 specimens were sampled, 121 from five sites in the Amazon basin and 111 from five sites in the Tocantins-Araguaia basin. The analyses investigated fragments of the Cytochrome b, Control Region, Cytochrome Oxidase I, NADH dehydrogenase subunit 2 and seven loci microsatellites. The analyses revealed the existence of two mitochondrial lineages within the general area, with no haplotypes shared between basins, and genetic variability significantly higher in the Amazon than in the Tocantins-Araguaia basin. Two divergent, but sympatric mitochondrial lineages were found in the Amazon basin, but only a single lineage in the Tocantins-Araguaia basin. The existence of these two mitochondrial lineages indicates that past events, probably occurring during the Pleistocene, resulted in the separation of the populations of this species and molded its evolutionary history, which is reflected directly in its mitochondrial DNA. The analysis of the arapaima population structure identified distinct levels of diversity within the distribution of the species, indicating specific geographic regions that will require special attention for the development of conservation and management strategies.

The arapaima (Arapaima gigas) is one of the most emblematic species of the Amazon region, and has a long history of exploitation. The present study investigated the connectivity and genetic variability of the arapaima in the region of the confluence of the Amazon and Araguaia-Tocantins basins, with emphasis on the population from the Lago Piratuba Biological Reserve, in the Brazilian state of Amapá. The study was based on the analysis of 11 microsatellite loci and the mtDNA control region sequences of 114 arapaima collected at six localities in the region of the eastern Amazon. The genetic analysis found significant differentiation, which indicated the presence of three distinct populations, the Lower Amazon-Marajó, Lago Piratuba, and Lower Tocantins populations, which lacked any significant level of gene flow. All three populations presented evidence of recent bottlenecks and distinct levels of genetic diversity, which was high only in the Lower Amazon-Marajó population. The conservation strategies for this region should consider the specific characteristics of these three populations and the different patterns of diversity found. The genetic characterization of the Lago Piratuba reserve as a unique population reinforces the importance of the implementation of adequate management strategies in the region.

Semipalmated sandpiper (Calidris pusilla) migration to the Southern Hemisphere includes a 5‐day non‐stop flight over the Atlantic Ocean, whereas semipalmated plover (Charadrius semipalmatus) migration, to the same area, is largely over land, with stopovers for feeding and rest. We compared the number and 3D morphology of hippocampal astrocytes of Ch. semipalmatus before and after autumnal migration with those of C. pusilla to test the hypothesis that the contrasting migratory flights of these species could differentially shape hippocampal astrocyte number and morphology. We captured individuals from both species in the Bay of Fundy (Canada) and in the coastal region of Bragança (Brazil) and processed their brains for selective GFAP immunolabeling of astrocytes. Hierarchical cluster analysis of astrocyte morphological features distinguished two families of morphological phenotypes, named type I and type II, which were differentially affected after migratory flights. Stereological counts of hippocampal astrocytes demonstrated that the number of astrocytes decreased significantly in C. pusilla, but did not change in Ch. semipalmatus. In addition, C. pusilla and Ch. semipalmatus hippocampal astrocyte morphological features were differentially affected after autumnal migration. We evaluated whether astrocyte morphometric variables were influenced by phylogenetic differences between C. pusilla and Ch. semipalmatus, using phylogenetically independent contrast approach, and phylogenetic trees generated by nuclear and mitochondrial markers. Our findings suggest that phylogenetic differences do not explain the results and that contrasting long‐distance migratory flights shape plasticity of type I and type II astrocytes in different ways, which may imply distinct physiological roles for these cells.

The two species of the genus Antilophia , Antilophia bokermanni and Antilophia galeata , are found in environments that are undergoing extensive modification, which may be provoking the loss of their genetic diversity. Nine polymorphic microsatellite loci were characterized and analyzed in each of these species. The distribution of allele frequencies revealed two clusters that reflected the distinct genetic profile of each species. Observed levels of heterozygosity were low for each species, with the lowest allelic diversity found in the critically endangered A. bokermanni . The set of loci described here, in contrast with other genetic markers that have been analyzed previously, effectively diagnosed the genetic diversity of different populations of the two species.