Alive Antillean manatee stranding is one of the main challenges for the conservation of the species in Brazil. In the present study, data on Antillean manatee stranding recorded by the CMA/ICMBio's Wild Animals Rehabilitation Center from 1987 to 2015 were analyzed. The CMA and the REMANE's (Northeastern Aquatic Mammal Stranding Network's) institutions have rescued on average five Antillean manatees per year. Approximately 56% of the animals were alive when rescued, and 43.7% were found dead. The states of Ceará and Rio Grande do Norte have the highest records of stranding, rescue, and assistance of alive calves. Stranding of alive specimens is more frequent during the austral summer, especially in January, February, and March. In the North region, the main threat to the Antillean manatee population seems to be interaction with fishing activities. Studies on the causes of dependent calf stranding in northeast Brazil are urgently needed to promote the development of public policies for the conservation of the species. Brazil's manatee rehabilitation centers must undergo improvements to better assist stranded calves, which need special care to survive.

1. The Antillean manatee (Trichechus manatus manatus), a subspecies of the West Indian manatee, is a large-bodied marine mammal found in fresh, brackish, and marine habitats throughout the Caribbean Islands and Central and South America. Antillean manatees in Brazil are classified as critically endangered, with a census size of approximately 500 individuals. The population in the Northeast region of Brazil is suspected to have approximately 300 manatees and is threatened by habitat alteration and incidental entanglement in fishing gear.2. A high incidence of dependent calf strandings have been identified near areas of altered critical manatee habitat. The majority of the calves are neonates, discovered alive, with no potential mothers nearby. These calves typically require human intervention to survive.3. Since 1989 the calves have been rescued (N=67), rehabilitated, and released (N=25) to supplement the small wild manatee population. The rescued calves, and those born in captivity, are typically, not released to their rescue location, mainly for logistical reasons. Therefore, phylogeographic analyses can help to identify related populations and appropriate release sites. 4. Here, mitochondrial DNA analyses identified low haplotype (h=0.08) and nucleotide (p=0.0026) genetic diversity in three closely related haplotypes. All three haplotypes (M01, M03, and a previously unidentified haplotype, M04) were found in the northern portion of the region, while only a single haplotype (M01) was represented in the south. This suggests the presence of two genetic groups with a central mixing zone. Release of rehabilitated calves to unrelated populations may result in genetic swamping of locally adapted alleles or genotypes, limiting the evolutionary potential of the population.5. The small population size coupled with low genetic diversity indicates that the Northeast Brazil manatee population is susceptible to inbreeding depression and possible local extinction. Further conservation measures incorporating genetic information could be beneficial to the critically endangered Brazilian manatee population.

The Antillean subspecies of the West Indian manatee is classified as endangered by the International Union for the Conservation of Nature (IUCN) Red List. In Brazil, the manatee population is listed as endangered with an estimated population size of 500–1,000. Historic hunting, recent habitat degradation, and fisheries bycatch have decreased the population size. The Amazonian manatee is listed as vulnerable by the IUCN with unknown population sizes within Brazil. The Antillean manatee occurs in sympatry with the Amazonian manatee in Brazil and hybridization has been previously indicated. To provide information on the genetic structure, diversity, and degree of hybridization in the sympatric zone near the Amazon River mouth, the mitochondrial DNA control region and 13 nuclear microsatellite markers were assessed on the two species. Samples were analyzed from the Antillean subspecies across its distribution in Brazil (n = 78) and from the Amazonian species (n = 17) at the Amazon River mouth and inland mainstem river. To assess the previously defined evolutionary significant units of Antillean manatees in the area, an additional 11 samples from Venezuela and Guyana were included. The Antillean manatee was found to be a single population in Brazil and had lower than average number of alleles (3.00), expected heterozygosity (0.34), and haplotype diversity (0.15) when compared to many other manatee populations. The low values may be influenced by the small population size and extended pressures from anthropogenic threats. Gene flow was identified with Venezuela/Guyana in admixed Antillean Brazil samples, although the two populations were found to be moderately divergent. The nuclear loci in Venezuela/Guyana Antillean manatee samples indicated high differentiation from the samples collected in the Amazon River (FST = 0.35 and RST = 0.18, p = 0.0001). No indication of nuclear hybridization was found except for a single sample, “Poque” that had been identified previously. The distribution of Antillean manatees in Brazil is extensive and the areas with unique habitat and threats would benefit from independent management and conservation actions. Gene flow, resulting in genetic diversity and long-term population stability, could be improved in the southern range through habitat restoration, and the establishments of travel corridors and protected areas, which are particularly important for successful parturition and neonatal calf survival.

Two species of manatees are found in Northern Brazil—the Antillean manatee (Trichechus manatus), which is found along the coast from Florida to Northeastern Brazil, and the Amazonian manatee (Trichechus inunguis), endemic to the Amazon drainage basin. These species show a sympatric distribution in the region of the Marajó Archipelago, an estuarine area surrounding the Amazon River mouth. There is evidence of the occurrence of interspecific hybrids in this area, based on mitochondrial DNA analyses, although the use of nuclear markers has not corroborated this proposal. Considering that these species show very distinct karyotypes, despite being closely related (2n = 48 in T. manatus and 2n = 56 in T. inunguis), hybrids would present distinct chromosome numbers. Based on this, we conducted cytogenetic analyses using classic and molecular techniques in three calves found stranded in the Marajó Island and Amapá coast. The results showed that one of them, morphologically classified as T. inunguis, presented the correspondent karyotype, with 2n = 56. However, the other two, which were phenotypically similar to T. manatus, showed 2n = 49. Despite the same diploid number, their G-banding patterns revealed some differences. The results of the distribution of some microsatellite sequences have also confirmed the heterozygosity of some chromosomal pairs in these two individuals. These results are the first indubitable confirmation of the occurrence of natural hybrids between T. manatus and T. inunguis, and also brings about some issues concerning the viability of hybrids, considering that these two individuals do not correspond to an F1 hybrid, but instead, both presented a possible F2 karyotype.

Great efforts have been made to preserve manatees. Recently, a hybrid zone was described between Trichechus inunguis (TIN) and the Trichechus manatus manatus (TMM) in the Amazon estuary. Cytogenetic data on these sirenians are limited, despite being fundamental to understanding the hybridization/introgression dynamics and genomic organization in Trichechus. We analyzed the karyotype of TMM, TIN, and two hybrid specimens (“Poque” and “Vitor”) by classical and molecular cytogenetics. G-band analysis revealed that TMM (2n = 48) and TIN (2n = 56) diverge by at least six Robertsonian translocations and a pericentric inversion. Hybrids had 2n = 50, however, with Autosomal Fundamental Number (FNA) = 88 in “Poque” and FNA = 74 in “Vitor”, and chromosomal distinct pairs in heterozygous; additionally, “Vitor” exhibited heteromorphisms and chromosomes whose pairs could not be determined. The U2 snDNA and Histone H3 multi genes are distributed in small clusters along TIN and TMM chromosomes and have transposable Keno and Helitron elements (TEs) in their sequences. The different karyotypes observed among manatee hybrids may indicate that they represent different generations formed by crossing between fertile hybrids and TIN. On the other hand, it is also possible that all hybrids recorded represent F1 and the observed karyotype differences must result from mechanisms of elimination.