Recent phylogeographic structure in a widespread ‘weedy’ Neotropical tree species,Cordia alliodora (Boraginaceae)

Aim Although hundreds of tree species have broad geographic ranges in the Neotropics, little is known about how such widespread species attained disjunct distributions around mountain, ocean and xeric barriers. Here, we examine the phylogeographic structure of a widespread and economically important tree, Cordia alliodora, to: (1) test the roles of vicariance and dispersal in establishing major range disjunctions, (2) determine which geographic regions and/or habitats contain the highest levels of genetic diversity, and (3) infer the geographic origin of the species. Location Twenty‐five countries in Central and South America, and the West Indies. Methods Chloroplast simple sequence repeats (cpSSR; eight loci) were assayed in 67 populations (240 individuals) sampled from the full geographic range of C. alliodora. Chloroplast (trnH–psbA) and nuclear (internal transcribed spacer, ITS) DNA sequences were sampled from a geographically representative subset. Genetic structure was determined with samova , structure and haplotype networks. Analysis of molecular variance (AMOVA) and rarefaction analyses were used to compare regional haplotype diversity and differentiation. Results Although the ITS region was polymorphic it revealed limited phylogeographic structure, and trnH–psbA was monomorphic. However, structure analysis of cpSSR variation recovered three broad demes spanning Central America (Deme 1), the Greater Antilles and the Chocó (Deme 2), and the Lesser Antilles and cis‐Andean South America (Deme 3). samova showed two predominant demes (Deme 1 + 2 and Deme 3). The greatest haplotype diversity was detected east of the Andes, while significantly more genetic variation was partitioned among trans‐Andean populations. Populations experiencing high precipitation seasonality (dry ecotype) had greater levels of genetic variation. Main conclusions Cordia alliodora displayed weak cis‐ and trans‐Andean phylogeographic structure based on DNA sequence data, indicative of historical dispersal around this barrier and genetic exchange across its broad range. The cpSSR data revealed phylogeographic structure corresponding to three biogeographic zones. Patterns of genetic diversity are indicative of an origin in the seasonally dry habitats of South America. Therefore, C. alliodora fits the disperser hypothesis for widespread Neotropical species. Dispersal is evident in the West Indies and the northern Andean cordilleras. The dry ecotype harbours genetic variation that is likely to represent the source for the establishment of populations under future warmer and drier climatic scenarios.     

Genetic diversity of the mangrove‐associated alga Bostrychia radicans/Bostrychia moritziana (Ceramiales,Rhodophyta) from southern Central America

Previous studies suggested that the biodiversity of the mangrove‐associated Bostrychia radicans/Bostrychia moritziana species complex on the Pacific coast of Central America, based on genetic and reproductive data, were low compared with similar areas on the Atlantic coast. Evolutionary scenarios were proposed based on either a recent introduction to the Pacific, or a more uniform environment leading to genetically connected populations and low differentiation between populations. We sampled more extensively in southern Mexico, Guatemala and El Salvador and sequenced the samples for the RuBisCo spacer. Our results show that genetic diversity is high in these populations. Many haplotypes retrieved are also found in the Atlantic Ocean (USA, Brazil), an observation not made before. Data suggest that populations are highly differentiated with little evidence of isolation‐by‐distance. The population at La Puntilla, El Salvador is highly differentiated from other populations. Data also suggest that diversity is reduced in a northerly direction, with only one haplotype, unique to Pacific Central America, found north of Chiapas, Mexico. This could be due to northern expansion of this unique genotype as sea surface temperatures ameliorated following the last glacial maximum. Our data do not support the previous proposition of low diversity in the east central Pacific and suggest that much of the Pacific Central America diversity is from before the closure of the Isthmus of Panama.     

Global population genetic structure of the starlet anemone <Emphasis Type="Italic">Nematostella vectensis</Emphasis>: multiple introductions and implications for conservation policy

Distinguishing natural versus anthropogenic dispersal of organisms is essential for determining the native range of a species and implementing an effective conservation strategy. For cryptogenic species with limited historical records, molecular data can help to identify introductions. Nematostella vectensis is a small, burrowing estuarine sea anemone found in tidally restricted salt marsh pools. This species’ current distribution extends over three coast lines: (i) the Atlantic coast of North America from Nova Scotia to Georgia, (ii) the Pacific coast of North America from Washington to central California, and (iii) the southeast coast of England. The 1996 IUCN Red List designates N. vectensis as “vulnerable” in England. Amplified fragment length polymorphism (AFLP) fingerprinting of 516 individuals from 24 N. vectensis populations throughout its range and mtDNA sequencing of a subsample of these individuals strongly suggest that anthropogenic dispersal has played a significant role in its current distribution. Certain western Atlantic populations of N. vectensis exhibit greater genetic similarity to Pacific populations or English populations than to other western Atlantic populations. At the same time, F-statistics showing high degrees of genetic differentiation between geographically proximate populations support a low likelihood for natural dispersal between salt marshes. Furthermore, the western Atlantic harbors greater genetic diversity than either England or the eastern Pacific. Collectively, these data clearly imply that N. vectensis is native to the Atlantic coast of North America and that populations along the Pacific coast and in England are cases of successful introduction.     

Land barriers and open oceans: effects on gene diversity and population structure in Avicennia germinans L. (Avicenniaceae)

Avicennia germinans L. is a widespread mangrove species occupying the west coast of Africa and the Atlantic and Pacific coasts of the Americas from the Bahamas to Brazil and Baja California to Peru. An amplified fragment length polymorphism (AFLP) molecular analysis was carried out to assess genetic architecture within this species and to evaluate the effects of the Atlantic Ocean and the Central American Isthmus (CAI) on population and regional genetic diversity and differentiation. In total, 349 polymorphic AFLP fragments were identified among 144 individuals from 14 populations from the east Atlantic, west Atlantic and east Pacific. Levels of genetic diversity varied considerably among populations, but were generally higher in populations from the east Atlantic. Regional differentiation between the Pacific coast and Atlantic populations was greater than between east and west Atlantic populations, suggesting that the CAI has had an important influence on population genetic structure in this species. The lower level of divergence of east Atlantic from west Atlantic populations suggests some dispersal across the Atlantic Ocean, although migration rates are probably low; Nm from GST equal to 0.41 and accumulation of private and rare alleles in the east Atlantic. Population differentiation did not appear to follow an isolation by distance model and has probably resulted from complex patterns of population bottlenecks, and founder events due to landscape changes during the Pleistocene, particularly in the west Atlantic. The molecular data provide no support for the treatment of east Atlantic populations as a separate species A. africana.     

Major Histocompatibility Complex (MHC) class II sequence polymorphism in long-finned pilot whale (Globicephala melas) from the North Atlantic

Determining how intra-specific genetic diversity is apportioned among natural populations is essential for detecting local adaptation and identifying populations with inherently low levels of extant diversity which may become a conservation concern. Sequence polymorphism at two adaptive loci (MHC DRA and DQB) was investigated in long-finned pilot whales (Globicephala melas) from four regions in the North Atlantic and compared with previous data from New Zealand (South Pacific). Three alleles were resolved at each locus, with trans-species allele sharing and higher levels of non-synonymous to synonymous substitution, especially in the DQB locus. Overall nucleotide diversities of 0.49?±?0.38% and 4.60?±?2.39% were identified for the DRA and DQB loci, respectively, which are relatively low for MHC loci in the North Atlantic, but comparable to levels previously described in New Zealand (South Pacific). There were significant differences in allele frequencies within the North Atlantic and between the North Atlantic and New Zealand. Patterns of diversity and divergence are consistent with the long-term effects of balancing selection operating on the MHC loci, potentially mediated through the effects of host-parasite coevolution. Differences in allele frequency may reflect variation in pathogen communities, coupled with the effects of differential drift and gene flow.     

Formation of population genetic structure following the introduction and establishment of non-native American shad (<Emphasis Type="Italic">Alosa sapidissima</Emphasis>) along the Pacific Coast of North America

Biological invasions provide opportunities to examine contemporary evolutionary processes in novel environments. American shad, an anadromous fish native to the Atlantic Coast of North America, was introduced to California in 1871 and established spawning populations along the Pacific Coast that may provide insights into the dynamics of dispersal, colonization, and the establishment of philopatry. Using 13 neutral microsatellite loci we genotyped anadromous, freshwater resident and landlocked American shad from 14 locations along the US Pacific Coast to resolve population genetic structure. We observed significant differences in multilocus allele frequency distributions in nearly all (61/66; 92%) pairwise comparisons of non-native anadromous, freshwater resident and landlocked populations, and detected significant genetic differentiation for most (55/66; 83%) of these comparisons. Genetic divergence between landlocked and anadromous populations is due to genetic drift in isolation because of a physical migration barrier. However, some reproductive isolating mechanism maintains genetic differentiation between sympatric populations in the Columbia River exhibiting alternative life history strategies (i.e. anadromous vs. ‘freshwater-type’). Non-native populations possessed genetic variants that were not observed in the species’ native range and were strongly differentiated from Atlantic Coast populations (\({\text{G}}^{{\prime }}_{\text{ST}}\)?=?0.218). Our results indicate that philopatry became established shortly after dispersal and colonization along the Pacific Coast. This study contributes to our understanding of dynamic evolutionary processes during invasions.     

Morphological and genetic evidence for two evolutionarily significant units (ESUs) in the South American fur seal, <Emphasis Type="Italic">Arctocephalus gazella</Emphasis>

The South American fur seal (Arctocephalus australis) is widely distributed, occurring along both the Atlantic and the Pacific coasts of South America. Previous work suggests there may be more than one subspecies, highlighting the need for further study. Here, we combine traditional and geometric morphometric analysis of skull shape and size with genetic data to compare two populations of South American fur seals, one from Uruguay and one from Peru. As a control group we used material from the closely related species Arctocephalus gazella. Both techniques of morphometric analysis reveal pronounced geographic variation in size and shape of the skull, with Peruvian specimens (n = 102) being larger than Uruguayan skulls (n = 133) and significant shape differences concentrated in the rostral region. Similarly, seven highly polymorphic microsatellite loci reveal highly significant differences in allele frequency. Moreover, Bayesian analysis implemented using the program structure reveals two separate clusters corresponding perfectly to the two populations, with an assignment test correctly placing over 98% of specimens in their population of origin. This degree of differentiation for both genetic and morphological traits suggests complete and possibly prolonged isolation to the extent that we believe these populations should be considered distinct evolutionarily significant units.     

Widespread gene flow between oceans in a pelagic seabird species complex

Global‐scale gene flow is an important concern in conservation biology as it has the potential to either increase or decrease genetic diversity in species and populations. Although many studies focus on the gene flow between different populations of a single species, the potential for gene flow and introgression between species is understudied, particularly in seabirds. The only well‐studied example of a mixed‐species, hybridizing population of petrels exists on Round Island, in the Indian Ocean. Previous research assumed that Round Island represents a point of secondary contact between Atlantic (Pterodroma arminjoniana) and Pacific species (Pterodroma neglecta and Pterodroma heraldica). This study uses microsatellite genotyping and tracking data to address the possibility of between‐species hybridization occurring outside the Indian Ocean. Dispersal and gene flow spanning three oceans were demonstrated between the species in this complex. Analysis of migration rates estimated using bayesass revealed unidirectional movement of petrels from the Atlantic and Pacific into the Indian Ocean. Conversely, structure analysis revealed gene flow between species of the Atlantic and Pacific oceans, with potential three‐way hybrids occurring outside the Indian Ocean. Additionally, geolocation tracking of Round Island petrels revealed two individuals travelling to the Atlantic and Pacific. These results suggest that interspecific hybrids in Pterodroma petrels are more common than was previously assumed. This study is the first of its kind to investigate gene flow between populations of closely related Procellariiform species on a global scale, demonstrating the need for consideration of widespread migration and hybridization in the conservation of threatened seabirds.     

Molecular taxonomy and population structure of the rough‐toothed dolphin Steno bredanensis (Cetartiodactyla: Delphinidae)

Several delphinid species have shown genetic population structure, both between and within ocean basins. We investigated genetic differentiation in the rough‐toothed dolphin, Steno bredanensis, using mitochondrial control region sequences from several localities worldwide (N = 112). Preliminary analyses indicated high levels of genetic differentiation between the Atlantic and Pacific/Indian Oceans, which were further investigated using complete cytochrome b sequences and mitogenomes. Phylogenetic analyses were inconclusive about the existence of cryptic speciation in the genus Steno. Notwithstanding this result, analysis of molecular variance and Φ‐statistics analyses revealed strong population differentiation not only between the Atlantic and Pacific, but also within the Atlantic, where three populations were detected: Caribbean, southeastern Brazil, and southern Brazil. We propose that these populations be considered management units for conservation purposes. Our results provide the first perspective on the worldwide genetic differentiation of S. bredanensis. © 2015 The Linnean Society of London     

Reproductive compatibility among Mexican populations of Anastrepha obliqua: theoretical and management implications

The fraterculus species group, composed of 34 species in the genus Anastrepha (Diptera: Tephritidae), includes the fraterculus cryptic species complex formed by eight reproductively isolated morphotypes. A previous study revealed six genetic mitochondrial types of Anastrepha obliqua, suggesting the existence of a second cryptic species complex. However, marked discrepancies between nuclear and mitochondrial loci rather suggest incomplete lineage sorting or introgression between A. obliqua and A. fraterculus. Such hybridization could nevertheless result in reproductive isolation, an outcome that could affect efficacy of area‐wide management for the most important pest of mangos in America. Two mitochondrial types occur in Mexico, and the limits of a third one, encompassing Central American populations, have not been clearly established. Here, we tested reproductive compatibility among three A. obliqua populations from the Pacific and a population from the Gulf of Mexico. No evidence of pre‐zygotic isolation was found. Flies from the Atlantic mated randomly for equal duration with individuals from three Pacific populations. Homotypic and heterotypic crosses produced similar numbers of eggs, with heterotypic crosses of Pacific males and Atlantic females hatching in lower proportions. Larvae of all cross types developed equally in mangos and exhibited no sex ratio distortion of hybrid F1. The three mitochondrial types identified in Mexico and Central America do not appear to be cryptic species and can be managed using one single strain for the sterile insect technique.     

Population genetic structure in Atlantic and Pacific Ocean common murres (Uria aalge): natural replicate tests of post‐Pleistocene evolution

Understanding the factors that influence population differentiation in temperate taxa can be difficult because the signatures of both historic and contemporary demographics are often reflected in population genetic patterns. Fortunately, analyses based on coalescent theory can help untangle the relative influence of these historic and contemporary factors. Common murres (Uria aalge) are vagile seabirds that breed in the boreal and low arctic waters of the Northern Hemisphere. Previous analyses revealed that Atlantic and Pacific populations are genetically distinct; however, less is known about population genetic structure within ocean basins. We employed the mitochondrial control region, four microsatellite loci and four intron loci to investigate population genetic structure throughout the range of common murres. As in previous studies, we found that Atlantic and Pacific populations diverged during the Pleistocene and do not currently exchange migrants. Therefore, Atlantic and Pacific murre populations can be used as natural replicates to test mechanisms of population differentiation. While we found little population genetic structure within the Pacific, we detected significant east–west structuring among Atlantic colonies. The degree that population genetic structure reflected contemporary population demographics also differed between ocean basins. Specifically, while the low levels of population differentiation in the Pacific are at least partially due to high levels of contemporary gene flow, the east–west structuring of populations within the Atlantic appears to be the result of historic fragmentation of populations rather than restricted contemporary gene flow. The contrasting results in the Atlantic and Pacific Oceans highlight the necessity of carefully considering multilocus nonequilibrium population genetic approaches when reconstructing the demographic history of temperate Northern Hemisphere taxa.     

Geographic distribution and diversity of mitochondrial DNA haplotypes in South American sea lions (Otaria flavescens) and fur seals (Arctocephalus australis)

Genetic diversity and population structure of two species of South American pinnipeds, Otaria flavescens and Arctocephalus australis, from colonies located along the south-eastern coast of South America, were analysed using mitochondrial DNA haplotypes and compared with two populations of these species from the Pacific coast. A 445 base-pair segment, that included the tRNA-Glu gene (31 bp) and the adjacent cytochrome b gene (414 bp), was amplified using the polymerase chain reaction and sequenced directly. O. flavescens and A. australis showed six and seven haplotypes with 12 and 20 polymorphic sites, respectively. In the Atlantic Ocean there was an individual of A. australis that showed an haplotype that was highly divergent from the others. If this haplotype is excluded, the pattern of haplotype differentiation obtained for both species indicated a possible bottleneck that would have occurred 110,000 years ago, which also affected other pinnipeds. Colonies of the Atlantic and the Pacific did not share haplotypes. This result, based on a limited number of samples for the comparisons between oceans, suggests that populations from both oceans correspond to different evolutionarily significant units. O. flavescens on the Atlantic coast shows two clusters of breeding colonies in Uruguay and Patagonia, separated by a thousand kilometres. Colonies within clusters did not show significant differences in haplotype frequencies, but the difference between the clusters was significant, suggesting that they correspond to different conservation stocks.     

Population genetic structure of the endangered crayfish Austropotamobius pallipes in France based on microsatellite variation: biogeographical inferences and conservation implications

1. One important goal in conservation biology is to characterise evolutionary lineages within endangered species before management decisions are taken. Here, we assess population differentiation in the freshwater crayfish Austropotamobius pallipes, an endangered species endemic to western Europe and provide valuable information for the conservation of French populations. 2. Analysis of five microsatellite loci in 44 populations revealed very different within population levels of genetic diversity (0.000 < H₀ < 0.564). Two groups, corresponding to northern and southern French populations, showed a high degree of genetic differentiation in both allele frequencies and allele sizes. Comparison of these results with previous studies of A. pallipes strongly suggests that the divergence between northern and southern populations could have occurred during the last glaciation period of the Pleistocene from one Atlantic and one Mediterranean refuge. 3. Evidence for genetic admixture between these two lineages was revealed by correspondence analyses in southern populations, probably as the result of artificial translocations. 4. French populations appeared significantly differentiated among the different river drainages and were highly structured within rivers. The impact of population size, population bottlenecks and founder events on the population genetic differentiation are discussed. 5. Based on these results, we propose the designation of two evolutionarily significant units for A. pallipes in France. Our data also support the maintenance of separate demographic management strategies for crayfish inhabiting different river systems. However, genetic analyses will have to be combined with demographic and ecological data for sustainable conservation programmes.     

Clarification and review of Lepidopilum affine and L. grevilleanum (Callicostaceae)

Lepidopilum grevilleanum Mitt., long considered a synonym ofL. affine C. Müll., is a distinct and rare species of western Ecuador.Lepidopilum affine is widespread, presently known from the western and northern Amazon basin, Atlantic region of northern South America, and the Pacific coastal region of Central America. Several new synonyms are proposed forLepidopilum affine: L. allionii Broth.,L. ambiguum Broth.,L. antisanense Bartr.,L. mittenii C. Müll.,L. obtusulum C. Müll., andL. subobtusulum Broth.Lepidopilum pulcherrimum Steere is a synonym ofL. grevilleanum.     

Genetic diversity enhanced by ancient introgression and secondary contact in East Pacific black mangroves

Regional distribution of genetic diversity in widespread species may be influenced by hybridization with locally restricted, closely related species. Previous studies have shown that Central American East Pacific populations of the wide-ranged Avicennia germinans , the black mangrove, harbour higher genetic diversity than the rest of its range. Genetic diversity in this region might be enhanced by introgression with the locally restricted Avicennia bicolor . We tested the hypotheses of ancient hybridization using phylogenetic analysis of the internal transcribed spacer region (ITS) of the nuclear ribosomal DNA and intergenic chloroplast DNA; we also tested for current hybridization by population level analysis of nuclear microsatellites. Our results unveiled ancient ITS introgression between a northern Pacific Central American A. germinans lineage and A. bicolor . However, microsatellite data revealed contemporary isolation between the two species. Polymorphic ITS sequences from Costa Rica and Panama are consistent with a zone of admixture between the introgressant ITS A. germinans lineage and a southern Central American lineage of A. germinans . Interspecific introgression influenced lineage diversity and divergence at the nuclear ribosomal DNA; intraspecific population differentiation and secondary contact are more likely to have enhanced regional genetic diversity in Pacific Central American populations of the widespread A. germinans .     

Population genetics of Cordia alliodora (Boraginaceae), a neotropical tree. 2. Mating system

A multilocus mixed mating model was used to evaluate the mating system of a natural population of Cordia alliodora (Boraginaceae), a neotropical tree. The population was highly outcrossed (t_m = 0.966 ± 0.027), in agreement with results from controlled crosses. Departures from the mixed mating model were evident, suggesting some nonrandom, correlated mating. Pollen pool heterogeneity and variation in estimates of individual outcrossing rates indicated that the population may be genetically substructured. Individual outcrossing rates obtained for the samples taken from within different parts of the same tree indicated reduced levels of outcrossing due to limited sampling of the pollen pool. The incompatibility mechanism in C. alliodora, combined with variation in flowering and stand density, appears to lead to both temporal and spatial substructuring of the population.     

An introduced population of Chorda asiatica (Chordaceae,Laminariales) in Puget Sound,Pacific coast of North America

Northeastern Pacific Ocean and northwestern Atlantic Ocean populations of Chorda species, which have not been examined in previous phylogenetic studies, were investigated. All specimens that were collected in Hood Canal, Puget Sound, WA, USA, Pacific coast of North America, showed identical ITS‐5.8S rDNA sequences, and they were included in the clade of Japanese Chorda asiatica. With morphological data added to the molecular data, they were identified as C. asiatica and were concluded to be non‐indigenous populations, most likely introduced with oyster spat together with Sargassum muticum. Specimens collected in New York, NY, USA, Atlantic coast of North America, were genetically closest to C. filum from Newfoundland and were identified as C. filum. The genetic divergence of the North Atlantic populations of C. filum was relatively small compared to that of Japanese C. asiatica considering their broader distributional ranges on both sides of the Atlantic.     

欧洲刺槐种源群体遗传结构和多样性

对来自欧洲和美国的 18个刺槐种源子代进行了等位酶分析。可进行遗传分析的 7个酶系统 (Amy,Fe,L ap,Idh,Mdh,6 Pgd,Skd)中有 14个基因位点 ,其中 12个位点具有多态性。每个多态位点平均等位基因数 (A/L )变化在 1.5 6～ 3.6 7之间 ,平均基因型数 (G/L)变化在 1.6 1～ 7.11之间 ,平均等位基因有效数目 (Ae)变化在 1.0 2～ 2 .5 0之间 ,预期杂合度 (H e)变化在0 .0 2～ 0 .5 6之间。不同种源群体之间也存在较大的遗传差异 ,在 8个德国种源中 ,各群体的 A、Ae、和 H e等相对较小 ,但不同群体间差异较大。各位点等位基因频率在不同种源群体间变化也较大 ,表明德国各种源群体内遗传变异相对较小 ,但群体间差异较大。来自匈牙利和斯洛伐克的 8个种源群则相反 ,各群体的 A、Ae、和 H e等相对较大 ,而不同种源群体间差异则较小 ,各位点等位基因频率在种源群体间变化相对一致 ,表明这两个国家的种源群体内变异较大 ,但不同种源群体间差异较小。欧洲的刺槐种源并未形成明显的地理变异模式 ,而且欧洲的种源和来自原产地的美国种源相比 ,没有发现明显的差异。经过 Hardy-Weinberg平衡检测证明 ,88.4 1%位点符合 H- W遗传平衡 ,表明各群体基因频率和基因型频率保持较高的稳定性 ,且种源内的变异大于种源间变异 ,94 .     

A geometric morphometric and microsatellite analyses of <Emphasis Type="Italic">Scaptotrigona mexicana</Emphasis> and <Emphasis Type="Italic">S. pectoralis</Emphasis> (Apidae: Meliponini) sheds light on the biodiversity of Mesoamerican stingless bees

Geometric morphometrics and molecular methods are effective tools to study the variability of stingless bee populations and species that merit protection given their worldwide decline. Based on previous evidence of cryptic lineages within the Scaptotrigona genus, we tested the existence of multiple evolutionary lineages within the species S. mexicana and we investigated the status of S. pectoralis. By analyzing their population structure, we found differences between the Pacific and Atlantic populations of each of these species, although geometric morphometrics of the wing only confirmed these results in S. mexicana. There was a tendency towards enhanced genetic differentiation over larger distances in the Atlantic populations of both species but not in the Pacific populations. These results revealed a pattern of differentiation among evolutionary units and a specific distribution of genetic diversity within these Scaptotrigona species in Mesoamerica, suggesting the need for future taxonomic revisions, as well as activities aimed at management and conservation.     

Geographic Microsatellite Variability in Central American Howling Monkeys

In 1997, we began to assess the genetic variability and the potential conservation risk of the increasing human impact on the howling monkeys of Ometepe Island in southern Nicaragua. We captured and collected blood from 29 howling monkeys (Alouatta palliata) at two geographically separated localities in a single area (San Ramon) on Ometepe Island, Nicaragua, during two field seasons. We also collected blood from a community of 10 Alouatta pigra in the Scotland Half Moon region in Belize. We extracted DNA from the blood and analyzed 12 microsatellite loci. The number of alleles per locus (allele variability) is less for most (but not all) loci in the Ometepe versus the Belize sample and less than earlier published reports of mixed geographic samples from Central America. The results are noteworthy in that both the Ometepe Island sample and the Belize sample possess greater allelic heterozygosity for most loci than reported in other Central American howling monkey populations. The Ometepe and Belize groups also demonstrated differences in allele frequencies at each geographic location. There appeared to be adequate gene flow in both locations despite extensive fragmentation due to agriculture and other human land usage.