Phylogeography of the West Indian manatee (Trichechus manatus): how many populations and how many taxa?

Vocalizations of wild West Indian manatee vary across subspecies and geographic location

Geographic variation in the vocal behavior of manatees has been reported but is largely unexplored. Vocalizations of wild West Indian manatees (Trichechus manatus) were recorded with hydrophones in Florida from Florida manatees (Trichechus manatus latirostris), and in Belize and Panama from Antillean manatees (Trichechus manatus manatus) to determine if calls varied between subspecies and geographic regions. Calls were visually classified into five categories: squeaks, high squeaks, squeals, squeak-squeals, and chirps. From these five categories, only three call types (squeaks, high squeaks and squeals) were observed in all three populations. Six parameters from the temporal and frequency domains were measured from the fundamental frequency of 2878 manatee vocalizations. A repeated measures PERMANOVA found significant differences for squeaks and high squeaks between each geographic location and for squeals between Belize and Florida. Almost all measured frequency and temporal parameters of manatee vocalizations differed between and within subspecies. Variables that may have influenced the variation observed may be related to sex, body size, habitat and/or other factors. Our findings provide critical information of manatee calls for wildlife monitoring and highlight the need for further study of the vocal behavior of manatees throughout their range.

The first assessment of the genetic diversity and structure of the endangered West Indian manatee in Cuba

The coastal waters of Cuba are home to a small, endangered population of West Indian manatee, which would benefit from a comprehensive characterization of the population's genetic variation. We conducted the first genetic assessment of Cuban manatees to determine the extent of the population's genetic structure and characterize the neutral genetic diversity among regions within the archipelago. We genotyped 49 manatees at 18 microsatellite loci, a subset of 27 samples on 1703 single nucleotide polymorphisms (SNPs), and sequenced 59 manatees at the mitochondrial control region. The Cuba manatee population had low nuclear (microsatellites H_E = 0.44, and SNP H_E = 0.29) and mitochondrial genetic diversity (h = 0.068 and π = 0.00025), and displayed moderate departures from random mating (microsatellite F_IS = 0.12, SNP F_IS = 0.10). Our results suggest that the western portion of the archipelago undergoes periodic exchange of alleles based on the evidence of shared ancestry and low but significant differentiation. The southeast Guantanamo Bay region and the western portion of the archipelago were more differentiated than southwest and northwest manatees. The genetic distinctiveness observed in the southeast supports its recognition as a demographically independent unit for natural resource management regardless of whether it is due to historical isolation or isolation by distance. Estimates of the regional effective population sizes, with the microsatellite and SNP datasets, were small (all N_e < 60). Subsequent analyses using additional samples could better examine how the observed structure is masking simple isolation by distance patterns or whether ecological or biogeographic forces shape genetic patterns.

Novel insights on aquatic mammal MHC evolution: Evidence from manatee DQB diversity

The low diversity in marine mammal major histocompatibility complex (MHC) appears to support the hypothesis of reduced pathogen selective pressure in aquatic systems compared to terrestrial environments. However, the lack of characterization of the aquatic and evolutionarily distant Sirenia precludes drawing more generalized conclusions. Therefore, we aimed to characterize the MHC DQB diversity of two manatee species and compare it with those reported for marine mammals. Our results identified 12 and 6 alleles in T. inunguis and T. manatus, respectively. Alleles show high rates of nonsynonymous substitutions, suggesting loci are evolving under positive selection. Among aquatic mammals, Pinnipeda DQB had smaller numbers of alleles, higher synonymous substitution rate, and a dN/dS ratio closer to 1, suggesting it may be evolving under more relaxed selection compared to fully aquatic mammals. This contradicts one of the predictions of the hypothesis that aquatic environments impose reduced pathogen pressure to mammalian immune system. These results suggest that the unique evolutionary trajectories of mammalian MHC may impose challenges in drawing ecoevolutionary conclusions from comparisons across distant vertebrate lineages.

Karyotypical Confirmation of Natural Hybridization between Two Manatee Species, Trichechus manatus and Trichechus inunguis

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.

Molecular confirmation of twinning in the West Indian Manatee (Trichechus manatus)

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.

Mitochondrial Genetic Diversity, Population Structure and Detection of Antillean and Amazonian Manatees in Colombia: New Areas and New Techniques

The Antillean manatee (Trichechus manatus) and the Amazonian manatee (Trichechus inunguis) are distributed in rivers in the Caribbean and Amazonian region of Colombia respectively. For 30 years, genetic information has been obtained from these populations in order to inform conservation programs for these endangered species and decide on the location to release them back to the wild. However, in previous studies, samples from rivers in some areas of the country were not included, given the difficulties to access these regions due to either logistic or safety issues. In this study, we analyzed mitochondrial DNA (mtDNA) control region (CR) sequences of from samples of T. manatus (n = 37) and T. inunguis (n = 4) (410 and 361 bp, respectively), obtained in new and previously unexplored rivers and bays in the country, including Santa Marta, Urabá Gulf, Ayapel Marsh (San Jorge River Basin), Meta River and Magdalena Medio and the low Magdalena River (Cesar Province and Canal del Dique) as well as additional samples from Puerto Nariño in the Colombian Amazon. Our results included the discovery of two newly described mtDNA CR haplotypes for T. manatus. In addition, we confirmed significant population differentiation at the mitochondrial level between the Magdalena and Sinú rivers and differentiation among areas of the same river, including the middle and low Magdalena River. This differentiation may be related to anthropic changes in the river since construction of the Canal del Dique in the XVI century. We also tested environmental DNA sampling and analyses techniques to evaluate its potential use for manatee detection and monitoring in bodies of water in Colombia, in order to evaluate new areas for future manatee conservation initiatives. We emphasize the need to continue using genetic information to provide evidence on the potential best locations to undertake animal release to prevent outbreeding depression.

TLR4 and TLR8 variability in Amazonian and West Indian manatee species from Brazil

Amazonian (Trichechus inunguis) and West Indian (Trichechus manatus) manatees are aquatic mammals vulnerable to extinction found in the Amazon basin and the coastal western Atlantic. Toll-like receptors (TLR) play a key role in recognizing pathogen-associated molecular patterns using leucine-rich repeats (LRRs). We described the diversity of TLR4 and TLR8 genes in these two species of manatee. Amazonian manatee showed seven SNPs in TLR4 and the eight in TLR8, while West Indian manatee shared four and six of those SNPs, respectively. In our analysis, TLR4 showed one non-conservative amino acid replacement substitution in LRR7 and LRR8, on the other hand, TLR8 was less variable and showed only conserved amino acid substitutions. Selection analysis showed that only one TLR4 site was subjected to positive selection and none in TLR8. TLR4 in manatees did not show any evidence of convergent evolution compared to species of the cetacean lineage. Differences in TLR4 and TLR8 polymorphism may be related to distinct selection by pathogens, population reduction of West Indian manatees, or an expected consequence of population expansion in Amazonian manatees. Future studies combining pathogen association and TLR polymorphism may clarify possible roles of these genes and be used for conservation purposes of manatee species.

The role of touch in captive and semi-captive Antillean manatees (Trichechus manatus manatus)

Tactile signals have been neglected in aquatic animal studies despite being a major communication modality. We investigated Antillean manatees’ tactile behavioural repertoire and budget in captivity (7-females and 4-males) and semi-captivity (4-males) in Brazil. We detected 17 tactile behaviours (14.03% of the activity budget) with social, self-maintenance, or environmental exploration functions. The observation method influenced the detection of self-maintenance behaviours — focal animal and ad libitum detected more of these behaviours than scan sampling. Age, sex, housing, and centre routines influenced the tactile repertoire. The captive females and semi-captive males tactile patterns differed, suggesting that sex and animal-pool density play a role in tactile patterns. We recommend carefully choosing the observation method when investigating functional categories of manatee tactile behaviours. The monitoring and stimulation of manatee tactile behaviours should integrate rehabilitation and reintroduction practices. Environmental enrichment may stimulate tactile behaviours related to habitat exploration, key behaviours in aiding manatee navigation.

Conservation issues using discordant taxonomic and evolutionary units: a case study of the American manatee (Trichechus manatus, Sirenia)

The delimitation of evolutionarily significant units (ESUs) frequently results in controversy, but prioritising populations with evolutionary independence is essential for effective in situ conservation management. The American manatee (Trichechus manatus) is distributed along subtropical and tropical coastal waters from Florida (USA) to Alagoas (Brazil), and two subspecies are traditionally recognised, namely, T. m. latirostris, restricted to the Florida peninsula, and T. m. manatus, found in the remaining areas. However, this subspecific classification is not supported by genetic and morphologic evidence, which, rather, recognises two deeply differentiated populations or ESUs called Atlantic (Brazil) and Caribbean (from Venezuela to Florida). In this viewpoint paper, we compare both intraspecific divisions of T. manatus and the conservation implications. First, we used all available mtDNA evidence to test the genealogical clustering of the two American manatee ESUs by using a tree-based coalescent method. Second, we have used different models under a coalescent framework to estimate the historic gene flow among manatee populations. The analysis of the spatial distribution of mtDNA clusters confirmed the existence of the two suggested ESUs, rather than the two claimed subspecies. Furthermore, the best model to explain historic migration indicates that Brazilian manatees belong to an isolated population, whereas Florida and Caribbean populations are connected by more recent gene flow. These results have confirmed that T. manatus of the Caribbean, Gulf of Mexico and Florida belong to the same deme or Caribbean ESU, and the relatively isolated population inhabiting the Atlantic coast of Brazil belongs to the Atlantic ESU. Furthermore, both ESUs are separated by an interspecific hybrid zone (with the Amazonian manatee) located around the mouth of the Amazon River towards the Guianas coastline. The subdivision of two ESUs is also highly supported by karyotypic, morphological and ecological data, and is in clear disagreement with the traditional subspecies designations and the IUCN priorities, which manages Brazilian manatees as part of the Antillean manatee subspecies (T. m. manatus). Rather, Brazilian manatees should be considered as a full priority for conservation and require further taxonomic research; because of their deep history of isolation, they present high genetic and morphologic differentiation from all other American manatees.

Updated and annotated checklist of recent mammals from Brazil

An updated and annotated checklist of mammals occurring in Brazil is presented. A total of 751 native species, distributed in 249 genera, 51 families and 11 orders were recorded to the country. The Brazilian mammalian fauna shows an elevated rate of endemism (30%; 223 species). Among the species evaluated by IUCN (668 species; 90%), a total of 80 (10.6% of total mammalian fauna) are Threatened, 28 (3.9%) are considered as Near Threatened, two species (0.3%) are presumable Extinct, 96 (12.8%) are considered with Deficient Data for conservation and 462 (61.6%) are considered as Least Concern. Fifteen new species were described since the last national compilation (published in 2017), which associated to new records to the country and synonimizations resulted in an increment of 30 species. Eight non-native species were introduced to the country, including the recently established Asiatic cervids Rusa unicolor (sambar) and Axis axis (chital). Seven native species (five primates and two hystricomorph rodents) have been translocated from their areas of natural occurrence to other areas inside the country.

Case report on helminth parasites of a necropsied Antillean manatee (Trichechus manatus manatus) in Belize

Sirenians are parasitized by a number of nematodes and trematodes, most which appear to be host specific. Reports of parasitism in the West Indian Manatee, Trichechus manatus, exist for several regions within the Atlantic Ocean, the Gulf of Mexico, and the Caribbean Sea, but there is a lack of parasitic data existing for the manatee subspecies living in the coastal waters of Belize. Herein, we report the first published record of parasites found in a deceased adult male Antillean manatee, Trichechus manatus manatus, recovered in the Placencia Lagoon, Belize. A thorough necropsy was performed which led to the identification of one nematode species, Heterocheilus tunicatus, and 2 species of trematode, Chiorchis groscofit, and Pulmonicola cochleotrema. The abundance of parasites found here appears to be within healthy limits given previous studies. Although our results are limited, the data provides supplemental information that can assist in-country and regional monitoring efforts for an endangered species.

History and conservation status of the Antillean manatee Trichechus manatus manatus in Hispaniola

To summarize the state of knowledge of the Endangered Antillean manatee Trichechus manatus manatus in Hispaniola, which comprises the Dominican Republic and Haiti, I reviewed documentary archives from pre-Columbian times to 2013. Manatees were historically abundant in Hispaniola but were hunted for centuries for their meat and other body parts for diverse uses. By the end of the 19th century manatees had become relatively rare around the island. Nevertheless, manatees remain widespread along the coast and occasionally occupy freshwater habitats in the Dominican Republic. In Haiti recent manatee sightings were restricted to two coastal areas. Currently, the manatee population of Hispaniola is perceived to be declining. The most commonly reported threats to the species include hunting, entanglement in fishing gear, boat strikes and disturbance by boat traffic, pollution, and habitat degradation and destruction. In the Dominican Republic longstanding national laws and international agreements protect the species and its habitat, and past conservation actions have raised public awareness about the status of the manatee. In Haiti knowledge of manatees is extremely limited and the species is not legally protected. I propose country-specific and binational recommendations to improve the contemporary conservation of manatees in the Dominican Republic and Haiti.

A hybrid swarm of manatees along the Guianas coastline, a peculiar environment under the influence of the Amazon River plume

The West Indian (Trichechus manatus) and Amazonian (T. inunguis) manatees have a sympatric occurrence at the mouth of the Amazon River. A result of this interspecific encounter is the occurrence of hybrids, which are frequently found along the coasts of Amapá state in Brazil, French Guiana and Guyana. Here we present new genetic evidence indicating the occurrence of a hybrid swarm along the Guianas Shield coastline, which is an interspecific hybrid zone that also separates T. manatus populations located east (Brazil) and west (Caribbean, Gulf of Mexico, Florida and Antilles). In addition, we suggest that this hybrid population occupies a peculiar mangrove-rich environment under strong influence of the Amazon River plume, which requires an independent management and should be considered a special conservation area.

Population estimates of Antillean manatees in Puerto Rico: an analytical framework for aerial surveys using multi-pass removal sampling

Effective management of the threatened Antillean manatee (Trichechus manatus manatus) in Puerto Rico requires reliable estimates of population size. Estimates are needed to assess population responses to management actions, and whether recovery objectives have been met. Aerial surveys have been conducted since 1976, but none adjusted for imperfect detection. We summarize surveys since 1976, report on current distribution, and provide population estimates after accounting for apparent detection probability for surveys between June 2010 and March 2014. Estimates in areas of high concentration (hotspots) averaged 317 ± 101, three times higher than unadjusted counts (104 ± 0.56). Adjusted estimates in three areas outside hotspots also differed markedly from counts (75 ± 9.89 versus 19.5 ± 3.5). Average minimum island-wide estimate was 386 ± 89, similar to the maximum estimate of 360 suggested in 2005, but fewer than the 700 recently suggested by the Puerto Rico Manatee Conservation Center. Manatees were more widespread than previously understood. Improving estimates, locally or island-wide, will require stratifying the island differently and greater knowledge about factors affecting detection probability. Sharing our protocol with partners in nearby islands (e.g., Cuba, Jamaica, Hispaniola), whose populations share genetic make-up, would contribute to enhanced regional conservation through better population estimates and tracking range expansion.

El manejo efectivo del manatí antillano amenazado en Puerto Rico requiere estimados de tamaños de poblaciónes confiables. Dichas estimaciones poblacionales son necesarias para evaluar las respuestas a las acciones de manejo, y para determinar si los objetivos de recuperación han sido alcanzados. Se han realizado censos aéreos desde 1976, pero ninguno de ellos han sido ajustados para detecciones imperfectas. Aquí resumimos los censos desde 1976, actualizamos la distribución, y reportamos los primeros estimados poblacionales ajustados para la probabilidad de detección aparente en los censos de Junio 2010 a Marzo 2014. Las estimaciones poblacionales en áreas de mayor concentración del manatí promedió 317 ± 103, tres veces más abundante que los conteos sin ajuste (104 ± 0.56). Las estimaciones poblacionales en tres áreas fuera de las áreas de mayor concentración del manatí también fueron marcadamente diferentes (75 ± 9.89 vs 19.5 ± 3.5). El estimado mínimo poblacional en la isla entera fue de 386 ± 89, similar al estimado máximo de 360 sugerido en el año 2005, pero menor a los 700 sugeridos recientemente por el Centro de Conservación de Manatíes de Puerto Rico. Documentamos que el manatí tiene una distribución más amplia de lo que se sabía con anterioridad. El mejoramiento de los estimados poblacionales locales o a nivel de isla requerirá que se estratifique a la isla en forma diferente y que se investiguen los factores que influencian a la probabilidad de detección. Compartir protocolos como este con colaboradores de islas vecinas (por. ej., Cuba, Jamaica, Española), cuyas poblaciones de manatíes comparten material genético, contribuiría a la conservación regional mediante mejores estimaciones poblacionales y monitoreo de la expansión de su ámbito doméstico.

Population Structure of Riverine and Coastal Dolphins Sotalia fluviatilis and Sotalia guianensis: Patterns of Nuclear and Mitochondrial Diversity and Implications for Conservation

Coastal and freshwater cetaceans are particularly vulnerable due to their proximity to human activity, localized distributions, and small home ranges. These species include Sotalia guianensis, found in the Atlantic and Caribbean coastal areas of central and South America, and Sotalia fluviatilis, distributed in the Amazon River and tributaries. We investigated the population structure and genetic diversity of these 2 species by analyses of mtDNA control region and 8-10 microsatellite loci. MtDNA analyses revealed strong regional structuring for S. guianensis (i.e., Colombian Caribbean vs. Brazilian Coast, FST = 0.807, ΦST = 0.878, P < 0.001) especially north and south of the Amazon River mouth. For S. fluviatilis, population structuring was detected between the western and eastern Amazon (i.e., Colombian Amazon vs. Brazilian Amazon, FST = 0.085, ΦST = 0.277, P < 0.001). Haplotype and nucleotide diversity were higher for S. fluviatilis. Population differentiation was supported by analysis of the microsatellite loci (S. guianensis, northern South America vs. southern South America FST = 0.275, Jost's D = 0.476, P < 0.001; S. fluviatilis, western and eastern Amazon FST = 0.197, Jost's D = 0.364, P < 0.001). Most estimated migration rates in both species overlapped with zero, suggesting no measurable migration between most of the sampling locations. However, for S. guianensis, there was measurable migration in neighboring sampling locations. These results indicate that the small home ranges of these species may act to restrict gene flow between populations separated by relatively short distances, increasing the risk of extirpation of some localized populations in the future if existing threats are not minimized.

Population differentiation and hybridisation of Australian snubfin (Orcaella heinsohni) and Indo-Pacific humpback (Sousa chinensis) dolphins in north-western Australia

Little is known about the Australian snubfin (Orcaella heinsohni) and Indo-Pacific humpback (Sousa chinensis) dolphins (‘snubfin’ and ‘humpback dolphins’, hereafter) of north-western Australia. While both species are listed as ‘near threatened’ by the IUCN, data deficiencies are impeding rigorous assessment of their conservation status across Australia. Understanding the genetic structure of populations, including levels of gene flow among populations, is important for the assessment of conservation status and the effective management of a species. Using nuclear and mitochondrial DNA markers, we assessed population genetic diversity and differentiation between snubfin dolphins from Cygnet (n = 32) and Roebuck Bays (n = 25), and humpback dolphins from the Dampier Archipelago (n = 19) and the North West Cape (n = 18). All sampling locations were separated by geographic distances >200 km. For each species, we found significant genetic differentiation between sampling locations based on 12 (for snubfin dolphins) and 13 (for humpback dolphins) microsatellite loci (F_ST = 0.05–0.09; P<0.001) and a 422 bp sequence of the mitochondrial control region (F_ST = 0.50–0.70; P<0.001). The estimated proportion of migrants in a population ranged from 0.01 (95% CI 0.00–0.06) to 0.13 (0.03–0.24). These are the first estimates of genetic diversity and differentiation for snubfin and humpback dolphins in Western Australia, providing valuable information towards the assessment of their conservation status in this rapidly developing region. Our results suggest that north-western Australian snubfin and humpback dolphins may exist as metapopulations of small, largely isolated population fragments, and should be managed accordingly. Management plans should seek to maintain effective population size and gene flow. Additionally, while interactions of a socio-sexual nature between these two species have been observed previously, here we provide strong evidence for the first documented case of hybridisation between a female snubfin dolphin and a male humpback dolphin.

Phylogeography and sex-biased dispersal across riverine manatee populations (Trichechus inunguis and Trichechus manatus) in South America

Phylogeographic patterns and sex-biased dispersal were studied in riverine populations of West Indian (Trichechus manatus) and Amazonian manatees (T. inunguis) in South America, using 410bp D-loop (Control Region, Mitochondrial DNA) sequences and 15 nuclear microsatellite loci. This multi-locus approach was key to disentangle complex patterns of gene flow among populations. D-loop analyses revealed population structuring among all Colombian rivers for T. manatus, while microsatellite data suggested no structure. Two main populations of T. inunguis separating the Colombian and Peruvian Amazon were supported by analysis of the D-loop and microsatellite data. Overall, we provide molecular evidence for differences in dispersal patterns between sexes, demonstrating male-biased gene flow dispersal in riverine manatees. These results are in contrast with previously reported levels of population structure shown by microsatellite data in marine manatee populations, revealing low habitat restrictions to gene flow in riverine habitats, and more significant dispersal limitations for males in marine environments.

Evidence of two genetic clusters of manatees with low genetic diversity in Mexico and implications for their conservation

The Antillean manatee (Trichechus manatus manatus) occupies the tropical coastal waters of the Greater Antilles and Caribbean, extending from Mexico along Central and South America to Brazil. Historically, manatees were abundant in Mexico, but hunting during the pre-Columbian period, the Spanish colonization and throughout the history of Mexico, has resulted in the significantly reduced population occupying Mexico today. The genetic structure, using microsatellites, shows the presence of two populations in Mexico: the Gulf of Mexico (GMx) and Chetumal Bay (ChB) on the Caribbean coast, with a zone of admixture in between. Both populations show low genetic diversity (GMx: N(A) = 2.69; H(E) = 0.41 and ChB: N(A) = 3.0; H(E) = 0.46). The lower genetic diversity found in the GMx, the largest manatee population in Mexico, is probably due to a combination of a founder effect, as this is the northern range of the sub-species of T. m. manatus, and a bottleneck event. The greater genetic diversity observed along the Caribbean coast, which also has the smallest estimated number of individuals, is possibly due to manatees that come from the GMx and Belize. There is evidence to support limited or unidirectional gene flow between these two important areas. The analyses presented here also suggest minimal evidence of a handful of individual migrants possibly between Florida and Mexico. To address management issues we suggest considering two distinct genetic populations in Mexico, one along the Caribbean coast and one in the riverine systems connected to the GMx.

The sixth rhino: a taxonomic re-assessment of the critically endangered northern white rhinoceros

Background

The two forms of white rhinoceros; northern and southern, have had contrasting conservation histories. The Northern form, once fairly numerous is now critically endangered, while the southern form has recovered from a few individuals to a population of a few thousand. Since their last taxonomic assessment over three decades ago, new material and analytical techniques have become available, necessitating a review of available information and re-assessment of the taxonomy.

Results

Dental morphology and cranial anatomy clearly diagnosed the southern and northern forms. The differentiation was well supported by dental metrics, cranial growth and craniometry, and corresponded with differences in post-cranial skeleton, external measurements and external features. No distinctive differences were found in the limited descriptions of their behavior and ecology. Fossil history indicated the antiquity of the genus, dating back at least to early Pliocene and evolution into a number of diagnosable forms. The fossil skulls examined fell outside the two extant forms in the craniometric analysis. Genetic divergence between the two forms was consistent across both nuclear and mitochondrial genomes, and indicated a separation of over a million years.

Conclusions

On re-assessing the taxonomy of the two forms we find them to be morphologically and genetically distinct, warranting the recognition of the taxa formerly designated as subspecies; Ceratotherium simum simum the southern form and Ceratotherium simum cottoni the northern form, as two distinct species Ceratotherium simum and Ceratotherium cottoni respectively. The recognition of the northern form as a distinct species has profound implications for its conservation.

Topographical organization of the facial motor nucleus in Florida manatees (Trichechus manatus latirostris)

Florida manatees (Trichechus manatus latirostris) possess modified vibrissae that are used in conjunction with specialized perioral musculature to manipulate vegetation for ingestion, and aid in the tactile exploration of their environment. Therefore it is expected that manatees possess a large facial motor nucleus that exhibits a complex organization relative to other taxa. The topographical organization of the facial motor nucleus of five adult Florida manatees was analyzed using neuroanatomical methods. Cresyl violet and hematoxylin staining were used to localize the rostrocaudal extent of the facial motor nucleus as well as the organization and location of subdivisions within this nucleus. Differences in size, length, and organization of the facial motor nucleus among mammals correspond to the functional importance of the superficial facial muscles, including perioral musculature involved in the movement of mystacial vibrissae. The facial motor nucleus of Florida manatees was divided into seven subnuclei. The mean rostrocaudal length, width, and height of the entire Florida manatee facial motor nucleus was 6.6 mm (SD 8 0.51; range: 6.2-7.5 mm), 4.7 mm (SD 8 0.65; range: 4.0-5.6 mm), and 3.9 mm (SD 8 0.26; range: 3.5-4.2 mm), respectively. It is speculated that manatees could possess direct descending corticomotorneuron projections to the facial motornucleus. This conjecture is based on recent data for rodents, similiarities in the rodent and sirenian muscular-vibrissal complex, and the analogous nature of the sirenian cortical Rindenkerne system with the rodent barrel system.

Phylogeography, phylogeny and hybridization in trichechid sirenians: implications for manatee conservation

Abstract The three living species of manatees, West Indian (Trichechus manatus), Amazonian (Trichechus inunguis) and West African (Trichechus senegalensis), are distributed across the shallow tropical and subtropical waters of America and the western coast of Africa. We have sequenced the mitochondrial DNA control region in 330 Trichechus to compare their phylogeographic patterns. In T. manatus we observed a marked population structure with the identification of three haplotype clusters showing a distinct spatial distribution. A geographic barrier represented by the continuity of the Lesser Antilles to Trinidad Island, near the mouth of the Orinoco River in Venezuela, appears to have restricted the gene flow historically in T. manatus. However, for T. inunguis we observed a single expanding population cluster, with a high diversity of very closely related haplotypes. A marked geographic population structure is likely present in T. senegalensis with at least two distinct clusters. Phylogenetic analyses with the mtDNA cytochrome b gene suggest a clade of the marine Trichechus species, with T. inunguis as the most basal trichechid. This is in agreement with previous morphological analyses. Mitochondrial DNA, autosomal microsatellites and cytogenetic analyses revealed the presence of hybrids between the T. manatus and T. inunguis species at the mouth of the Amazon River in Brazil, extending to the Guyanas and probably as far as the mouth of the Orinoco River. Future conservation strategies should consider the distinct population structure of manatee species, as well as the historical barriers to gene flow and the likely occurrence of interspecific hybridization.

Phylogeography and population genetics of the endangered Amazonian manatee, Trichechus inunguis Natterer, 1883 (Mammalia, Sirenia)

We used mitochondrial DNA control region sequences to examine phylogeography and population differentiation of the endangered Amazonian manatee Trichechus inunguis. We observe lack of molecular differentiation among localities and we find weak association between geographical and genetic distances. However, nested clade analysis supports restricted gene flow and/or dispersal with some long-distance dispersal. Although this species has a history of extensive hunting, genetic diversity and effective population sizes are relatively high when compared to the West Indian manatee Trichechus manatus. Patterns of mtDNA haplotype diversity in T. inunguis suggest a genetic disequilibrium most likely explained by demographic expansion resulting from secession of hunting and enforcement of conservation and protective measures. Phylogenetic analysis of T. manatus and T. inunguis haplotypes suggests that T. inunguis is nested within T. manatus, effectively making T. manatus a paraphyletic entity. Paraphyly of T. manatus and recent divergence times of T. inunguis and the three main T. manatus lineages suggest a possible need for a taxonomic re-evaluation of the western Atlantic Trichechus.

The evolution and phylogeography of the African elephant inferred from mitochondrial DNA sequence and nuclear microsatellite markers

Recent genetic results support the recognition of two African elephant species: Loxodonta africana, the savannah elephant, and Loxodonta cyclotis, the forest elephant. The study, however, did not include the populations of West Africa, where the taxonomic affinities of elephants have been much debated. We examined mitochondrial cytochrome b control region sequences and four microsatellite loci to investigate the genetic differences between the forest and savannah elephants of West and Central Africa. We then combined our data with published control region sequences from across Africa to examine patterns at the continental level. Our analysis reveals several deeply divergent lineages that do not correspond with the currently recognized taxonomy: (i) the forest elephants of Central Africa; the forest and savannah elephants of West Africa; and (iii) the savannah elephants of eastern, southern and Central Africa. We propose that the complex phylogeographic patterns we detect in African elephants result from repeated continental-scale climatic changes over their five-to-six million year evolutionary history. Until there is consensus on the taxonomy, we suggest that the genetic and ecological distinctness of these lineages should be an important factor in conservation management planning.

The evolutionary enigma of bonefishes (Albula spp.): cryptic species and ancient separations in a globally distributed shorefish

Many examples of cryptic marine species have been demonstrated with biochemical and molecular studies. In most cases, a broadly distributed taxon is actually a group of sibling species that can be distinguished (upon closer examination) by ecological or morphological characters. Fishes of the family Albulidae constitute a notable exception. Bonefish (Albula spp.) morphology and ecology are highly conserved around the globe, and their extended pelagic larval stage could allow population connections on a vast geographic scale. Based on this perceived homogeneity, bonefishes were classified as a single pantropical species, A. vulpes. However, allozyme studies of Hawaiian populations indicated that two sympatric species (A. glossodonta and A. neoguinaica) are included in the synonymy of A. vulpes. To ascertain the number and distribution of evolutionary partitions in Albula, we surveyed 564 bp of mitochondrial DNA (mtDNA) cytochrome b from 174 individuals collected at 26 locations. Sequence comparisons reveal eight deep lineages (d = 5.56-30.6%) and significant population structure within three of the four lineages that could be tested (phiST = 0.047-0.678). These findings confirm the genetic distinctiveness of the three species noted above and invoke the possibility of five additional species. Clock estimates for mtDNA indicate that these putative species arose 4-20 million years ago. Distinct evolutionary lineages coexist in several sample locations, yet show little morphological or ecological differentiation in sympatry. Thus, bonefish species seem to defy the evolutionary conventions of morphological differentiation over time and ecological displacement in sympatry. Despite multiple cases of sympatry, sister-taxa relationships inferred from mtDNA indicate that divergence in allopatry has been the predominant speciation mechanism in Albula. Stabilizing selection in the homogeneous habitat occupied by bonefishes (tropical sand flats) could promote the retention of highly conserved morphology and ecology.

The Central American squirrel monkey (Saimiri oerstedii): introduced hybrid or endemic species?

Although squirrel monkeys (Saimiri spp., Primates: Cebidae) are abundant and widespread in South America, the disjunct Central American species, Saimiri oerstedii, has been restricted to the Pacific wet lowlands of Costa Rica and Panama since the earliest historical records. This taxon is now endangered in Costa Rica and nearly extinct in Panama because of habitat loss, development, and the pet trade. Conservation efforts have been hampered because of the influential, but untested, speculation that S. oerstedii represents a hybrid species introduced by prehispanic Amerind traders from multiple localities in South America. Using nuclear and mitochondrial DNA sequence data to reconstruct the phylogenetic relationships among Saimiri from Central and South America, we reexamine the taxonomic status of squirrel monkeys from different geographic regions. The sequence data support P. Hershkovitz's (1984, Am. J. Primatol. 6: 257-281) taxonomy advocating four distinct species. Combining this information with evidence from the fossil record to date the divergence times among sister taxa, we test and reject the hypothesis that Central American squirrel monkeys are the result of human introduction.

Mitochondrial DNA variation, phylogeography and population structure of the Asian elephant

We report the first genetic analysis of free-ranging Asian elephants (Elephas maximus). We sampled 118 elephants from Sri Lanka, Bhutan/North India, and Laos/Vietnam by extracting DNA from dung, PCR amplifying and sequencing 630 nucleotides of mitochondrial DNA, including part of the variable left domain of the control region. Comparison with African elephant (Loxodonta africana) sequences indicated a relatively slow molecular clock in the Proboscidea with a sequence divergence of approximately 1%/Myr. Genetic diversity within Asian elephants was low, suggesting a small long-term effective population size. Seventeen haplotypes were identified within Asian elephants, which clustered into two well-differentiated assemblages with an estimated Pliocene divergence of 2.5-3.5 million years ago. The two assemblages showed incomplete geographical partitioning, suggesting allopatric divergence and secondary admixture. On the mainland, little genetic differentiation was observed between elephant populations of Bhutan and India or Laos and Vietnam. A significant difference in haplotype frequencies but relatively weak subdivision was observed between the regions Bhutan-India and Laos-Vietnam. Significant genetic differentiation was observed between the mainland and Sri Lanka, and between northern, mid-latitude and southern regions in Sri Lanka.

Preserving genes, species, or ecosystems? Healing the fractured foundations of conservation policy

The scientific foundations of conservation policy are the subject of a recent tripolar debate, with systematists arguing for the primacy of phylogenetic rankings, ecologists arguing for protection at the level of populations or ecosystems, and evolutionary biologists urging more attention for the factors that enhance adaptation and biodiversity. In the field of conservation genetics, this controversy is manifested in the diverse viewpoints of molecular systematists, population biologists, and evolutionary (and quantitative) geneticists. A resolution of these viewpoints is proposed here, based on the premise that preserving particular objects (genes, species, or ecosystems) is not the ultimate goal of conservation. In order to be successful, conservation efforts must preserve the processes of life. This task requires the identification and protection of diverse branches in the tree of life (phylogenetics), the maintenance of life-support systems for organisms (ecology), and the continued adaptation of organisms to changing environments (evolution). None of these objectives alone is sufficient to preserve the threads of life across time. Under this temporal perspective, molecular genetic technologies have applications in all three conservation agendas; DNA sequence comparisons serve the phylogenetic goals, population genetic markers serve the ecological goals, quantitative genetics and genome explorations serve the evolutionary goals.