Diversification in wild populations of the model organism Anolis carolinensis: A genome‐wide phylogeographic investigation

The green anole (Anolis carolinensis) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary history in association with morphological, physiological, or reproductive biology studies among sampling localities and necessitate increased effort to resolve evolutionary relationships among natural populations. Here, we used anchored hybrid enrichment of hundreds of genetic markers across the genome of A. carolinensis and identified five strongly supported phylogeographic groups. Using multiple analyses, we produced a fully resolved species tree, investigated relative support for each lineage across all gene trees, and identified mito‐nuclear discordance when comparing our results to previous studies. We found fixed differences in only one clade—southern Florida restricted to the Everglades region—while most polymorphisms were shared between lineages. The southern Florida group likely diverged from other populations during the Pliocene, with all other diversification during the Pleistocene. Multiple lines of support, including phylogenetic relationships, a latitudinal gradient in genetic diversity, and relatively more stable long‐term population sizes in southern phylogeographic groups, indicate that diversification in A. carolinensis occurred northward from southern Florida.     

Genetic differentiation in natural populations of a Keystone Bunchgrass (<Emphasis Type="Italic">Aristida stricta</Emphasis>) across its native range

Aristida stricta Michx. (Poaceae) is a perennial bunchgrass native to the Southeastern Coastal Plain of North America where it is a keystone species in the longleaf pine savannas and slash pine flatwoods from southeastern North Carolina to Florida, and westward to the coast of Mississippi. We examined genetic relationships within and among ten populations of A. stricta by using eight inter-simple sequence repeat (ISSR) markers to generate band frequency data for 32 individuals from each sampled population. An analysis of molecular variance showed that 38% of the variation resided among populations while 62% was attributable to variation within populations. Grouping the populations by habitat or by geographic location did not show significant differentiation between the groups. Overall, pair-wise geographic and genetic distances were not correlated. Data indicate that while individuals within each population are genetically diverse, there seemingly are barriers to gene flow across populations leading to their divergence. Each population contains several exclusive loci suggesting that limited gene flow and/or genetic drift are likely leading to this pattern of localization. Our results, coupled with those of the previous studies that presented evidence for local adaptation and phenotypic differences among populations, suggest that there is sufficient differentiation among populations of this species to warrant: (1) maintenance of the existing genetic diversity at individual sites, and (2) use of local seed and plant sources for conservation projects.     

Phylogeography of the fungal pathogen Histoplasma capsulatum

Until recently, Histoplasma capsulatum was believed to harbour three varieties, var. capsulatum (chiefly a New World human pathogen), var. duboisii (an African human pathogen) and var. farciminosum (an Old World horse pathogen), which varied in clinical manifestations and geographical distribution. We analysed the phylogenetic relationships of 137 individuals representing the three varieties from six continents using DNA sequence variation in four independent protein‐coding genes. At least eight clades were idengified: (i) North American class 1 clade; (ii) North American class 2 clade; (iii) Latin American group A clade; (iv) Latin American group B clade; (v) Australian clade; (vi) Netherlands (Indonesian?) clade; (vii) Eurasian clade and (viii) African clade. Seven of eight clades represented genetically isolated groups that may be recognized as phylogenetic species. The sole exception was the Eurasian clade which originated from within the Latin American group A clade. The phylogenetic relationships among the clades made a star phylogeny. Histoplasma capsulatum var. capsulatum individuals were found in all eight clades. The African clade included all of the H. capsulatum var. duboisii individuals as well as individuals of the other two varieties. The 13 individuals of var. farciminosum were distributed among three phylogenetic species. These findings suggest that the three varieties of Histoplasma are phylogenetically meaningless. Instead we have to recognize the existence of genetically distinct geographical populations or phylogenetic species. Combining DNA substitution rates of protein‐coding genes with the phylogeny suggests that the radiation of Histoplasma started between 3 and 13 million years ago in Latin America.     

Mitochondrial pseudo-control region in old world eagles (genus Aquila)

The mitochondrial pseudo-control region was analysed in five species of Aquila eagles. Indels caused great length differences in the nonrepetitive part of the region, whereas tandem repeat units were highly conserved among the genus. In a reconstructed phylogenetic tree, the clade formed by A. clanga and A. pomarina showed approximately the same distance to A. chrysaetos as did the clade A. heliaca/nipalensis. In Estonian subpopulations, 12 haplotypes were found among 51 A. pomarina individuals and 7 haplotypes among 8 A. clanga individuals. Nucleotide diversity in A. clanga was greater, and may be caused by decreased breeding density or by gene flow from other subpopulations.     

Phylogenetics of Planipapillus, lawn-headed onychophorans of the Australian Alps, based on nuclear and mitochondrial gene sequences

We addressed phylogenetic relationships among species of Planipapillus, a clade of oviparous onychophorans from southeastern mainland Australia, to create a framework for understanding the evolution of the modified male head papillae used in mating in this clade. We sequenced fragments of two mitochondrial genes, COI and 12S rRNA, and a nuclear intron from the fushi tarazu gene, for individuals from 14 putative species of Planipapillus and six outgroups. We analyzed these data under both parsimony and likelihood criteria, incorporating heterogeneous parameter fitting guided by likelihood ratio tests. These analyses result in strong, congruent support for many clades. We infer multiple independent origins of spikes in Planipapillus male head structures.     

Molecular phylogenetic analysis of the Grey-cheeked Fulvetta (Alcippe morrisonia) of China and Indochina: a case of remarkable genetic divergence in a "species"

The Grey-cheeked Fulvetta, Alcippe morrisonia, is a polytypic species of Quaker babbler (Timaliidae) occurring mainly in highlands from Burma across southern China to Taiwan. To examine gene flow among populations, we sequenced the mitochondrial ND2 gene of 39 individuals of six of the seven subspecies, plus multiple individuals of three outgroup Alcippe species. A lack of shared haplotypes and high FST values suggested no gene flow among populations. The nucleotide divergence between geographically juxtaposed subspecies ranged from 0.8% between Guangdong and Hainan to 9.4% between Yunnan and Vietnam. Phylogenetic analysis of the populations yielded a well resolved tree with two major clades. One clade consisted of the geographically central subspecies schaefferi and davidi, which are located largely in the "Mid-central" zoogeographic region of China's "Oriental" realm. The other clade, the geographically peripheral group, consisted of all other A. morrisonia subspecies, as well as an erstwhile outgroup, the Mountain Fulvetta (Alcippe peracensis annamensis) from central Vietnam. This peripheral group was further divided into two clades, one consisting of taxa occurring in China's "Southwest" zoogeographic region (fratercula and A. p. annamensis), and one occurring in China's "Southern" region (morrisonia, rufescentior, and hueti). These three geographic and phylogenetic groups represent at least four different species based on plumage differences and genetic differentiation. The phylogeny provides the first avian molecular evidence of area relationships among China's zoogeographic zones. It also highlights a remarkable and unexpected amount of genetic divergence and structure in a Sino-Indian "species". If such diversity occurs in other groups of birds with similar distribution, the ramifications are important for conservation planning.     

Genetic and phylogenetic divergence of feline immunodeficiency virus in the puma (Puma concolor).

Feline immunodeficiency virus (FIV) is a lentivirus which causes an AIDS-like disease in domestic cats (Felis catus). A number of other felid species, including the puma (Puma concolor), carry a virus closely related to domestic cat FIV. Serological testing revealed the presence of antibodies to FIV in 22% of 434 samples from throughout the geographic range of the puma. FIV-Pco pol gene sequences isolated from pumas revealed extensive sequence diversity, greater than has been documented in the domestic cat. The puma sequences formed two highly divergent groups, analogous to the clades which have been defined for domestic cat and lion (Panthera leo) FIV. The puma clade A was made up of samples from Florida and California, whereas clade B consisted of samples from other parts of North America, Central America, and Brazil. The difference between these two groups was as great as that reported among three lion FIV clades. Within puma clades, sequence variation is large, comparable to between-clade differences seen for domestic cat clades, allowing recognition of 15 phylogenetic lineages (subclades) among puma FIV-Pco. Large sequence divergence among isolates, nearly complete species monophyly, and widespread geographic distribution suggest that FIV-Pco has evolved within the puma species for a long period. The sequence data provided evidence for vertical transmission of FIV-Pco from mothers to their kittens, for coinfection of individuals by two different viral strains, and for cross-species transmission of FIV from a domestic cat to a puma. These factors may all be important for understanding the epidemiology and natural history of FIV in the puma.     

Insight into the population structure of hardhead silverside,Atherinomorus stipes (Teleostei: Atherinidae), in Belize and the Florida Keys using nd2

Little is known about the natural history, biology, and population genetic structure of the Hardhead Silverside, Atherinomorus stipes, a small schooling fish found around islands throughout the Caribbean. Our field observations of A. stipes in the cays of Belize and the Florida Keys found that populations tend to be in close association with the shoreline in mangrove habitats. Due to this potential island‐based population structuring, A. stipes represents an ideal system to examine questions about gene flow and isolation by distance at different geographic scales. For this study, the mitochondrial gene nd2 was amplified from 394 individuals collected from seven different Belizean Cays (N = 175) and eight different Floridian Keys (N = 219). Results show surprisingly high haplotype diversity both within and between island‐groups, as well as a high prevalence of unique haplotypes within each island population. The results are consistent with models that require gene flow among populations as well as in situ evolution of rare haplotypes. There was no evidence for an isolation by distance model. The nd2 gene tree consists of two well‐supported monophyletic groups: a Belizean‐type clade and a Floridian‐type clade, indicating potential species‐level differentiation.     

Phylogeny of the Procyonidae (Mammalia: Carnivora): molecules, morphology and the Great American Interchange

The Procyonidae (Mammalia: Carnivora) have played a central role in resolving the controversial systematics of the giant and red pandas, but phylogenetic relationships of species within the family itself have received much less attention. Cladistic analyses of morphological characters conducted during the last two decades have resulted in topologies that group ecologically and morphologically similar taxa together. Specifically, the highly arboreal and frugivorous kinkajou (Potos flavus) and olingos (Bassaricyon) define one clade, whereas the more terrestrial and omnivorous coatis (Nasua), raccoons (Procyon), and ringtails (Bassariscus) define another clade, with the similar-sized Nasua and Procyon joined as sister taxa in this latter group. These relationships, however, have not been tested with molecular sequence data. We examined procyonid phylogenetics based on combined data from nine nuclear and two mitochondrial gene segments totaling 6534bp. We were able to fully resolve relationships within the family with strongly supported and congruent results from maximum parsimony, maximum likelihood, minimum evolution, and Bayesian analyses. We identified three distinct lineages within the family: a (Nasua, Bassaricyon) clade, a (Bassariscus, Procyon) clade, and a Potos lineage, the last of which is sister to the other two clades. These findings, which are in strong disagreement with prior fossil and morphology-based assessments of procyonid relationships, reemphasize the morphological and ecological flexibility of these taxa. In particular, morphological similarities between unrelated genera possibly reflect convergence associated with similar lifestyles and diets rather than ancestry. Furthermore, incongruence between the molecular supermatrix and a morphological character matrix comprised mostly of dental characters [Baskin, J.A., 2004. Bassariscus and Probassariscus (Mammalia, Carnivora, Procyonidae) from the early Barstovian (Middle Miocene). J. Vert. Paleo. 24, 709-720] may be due to non-independence among atomized dental characters that does not take into account the high developmental genetic correlation of these characters. Finally, molecular divergence dating analyses using a relaxed molecular clock approach suggest that intergeneric and intrageneric splits in the Procyonidae mostly occurred in the Miocene. The inferred divergence times for intrageneric splits for several genera whose ranges are bisected by the Panamanian Isthmus is significant because they suggest diversification well precedes the Great American Interchange, which has long been considered a primary underlying mechanism for procyonid evolution.     

Phylogenetic divergence in leatherside chub (Gila copei) inferred from mitochondrial cytochrome b sequences

We examined intra-specific phylogenetic relationships in leatherside chub, Gila copei. The complete mitochondrial (mt) cytochrome b gene (1140 bp) was sequenced for 30 individuals from 10 populations that span the geographical distribution of this species. Traditional phylogenetic analyses revealed two deeply divergent and evolutionarily distinct mtDNA clades that are geographically separated in northern and southern drainage basins. Interpopulation sequence variation between clades ranged from 7.7 to 8.1%. The northern clade was genetically more similar and phylogenetically more closely related to the selected out-group Lepidomeda m. mollispinus than to the southern clade, suggesting that the taxonomy of this species may require revision. Sequence variation among populations within clades ranged from 0 to 0.3% in the north and from 0 to 0.7% in the south. Statistical parsimony was used to construct phylogenetic networks of haplotypes within clades. Nested clade analysis revealed that geographical fragmentation has played an important role in genetic structuring within northern and southern clades.     

Shallow genetic and morphological divergence among seaperches in the South Pacific (family Scorpaenidae; genus Helicolenus)

The phylogenetic relationships among populations of seaperch, Helicolenus spp., in the south-west Pacific were examined with mtDNA markers. Parts of the cytochrome b gene [459 base pair (bp)] and the control region (448 bp) were sequenced in 58 specimens from the south-west Pacific and four specimens of Helicolenus lengerichi from Chile. Only one clade was recognized in New Zealand coastal waters, despite a wide range of colour morphs. This clade also occurred in the mid Tasman Sea on the Norfolk Ridge and around Tasmania and Victoria. A second sympatric clade was identified around Tasmania and Victoria and to the west of New Zealand. A third allopatric clade was identified to the north of New Zealand and in deep water on the Chatham Rise and a fourth clade on the Foundation Seamounts and the Louisville Ridge. Helicolenus lengerichi from Chile formed a fifth clade. Assuming a molecular clock, the clades were estimated to have diverged c. 0·7–2·6 million years ago. Only two clades, around Tasmania and Victoria, were separated using morphology, colour (in live) and dorsal-fin soft ray counts and were confirmed as Helicolenus percoides and Helicolenus barathri . Two characters, orbit diameter and colour variation, previously used to identify two species in New Zealand waters were unreliable characters for species discrimination. Principle component analyses of 11 morphological measures from 67 individuals did not delineate the clades. A canonical discriminant analysis was able to separate four of the five clades, but mean discriminate probabilities were low (77·6%), except for the five Chilean specimens of H. lengerichi (100%).     

Origin of the green iguana (Iguana iguana) invasion in the greater Caribbean Region and Fiji

Invasive populations of green iguanas (Iguanidae: Iguana iguana) are widely established beyond their native Central, South American, and Lesser Antillean range in various islands of the Pacific, Florida USA, and in the Greater Caribbean Region. Although widespread, information about these invasions is scarce. Here we determine the origin of invasive populations of green iguanas in Puerto Rico, Fiji, The Caymans, Florida USA, The Dominican Republic, the US Virgin Islands (USVI) of St. Thomas and St. Croix, and a U.S.A pet store. We sampled 120 individuals from these locations and sequenced one mitochondrial (ND4) and two nuclear (PAC and NT3) loci. We also include a preliminary characterization of population structure throughout Puerto Rico using six microsatellite loci to genotype individuals across 10 sampling sites. Comparing the genealogical relationships of all our samples to published sequencing data from the native range, we found that sampled populations were largely a product of populations from Colombia and El Salvador; two countries with multiple, industrial-size pet iguana farming operations. Notably, we found that haplotypes detected exclusively in the USVI and Puerto Rico’s outlying island of Vieques are closely linked to green iguanas native to Saba and Montserrat (Lesser Antilles); a clade not reported in the pet trade. Our population genetic analyses did not reveal isolation among sampling sites in Puerto Rico, rather the evidence supported admixture across the island. This study highlights the roles of the pet trade and lack of regulation in the spread of green iguanas beyond their native range.

     

DNA barcoding reveals cryptic diversity in the peanut worm Sipunculus nudus

Peanut worm (Sipunculus nudus) is a cosmopolitan species mainly distributed in tropical and subtropical coastal waters. Analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene sequences among S. nudus from GenBank revealed high genetic variation (p‐distance, 0.115–0.235; k2p, 0.128–0.297) and paraphyletic relationships. These indicated misidentification and/or cryptic diversity may be present in the genus Sipunculus. To understand the genetic diversity and to manage the recourse of S. nudus, we collected specimens from coastal waters of southern China and Taiwan. In the phylogenetic topology, specimens can be separated into four distinct clades; three of these clades (clade A, B and C) were only represented from this region (southern China and Taiwan), but the clade D grouped with individuals from Central America (Atlantic coast). Furthermore, individuals of clades A and D were collected at the same location, which does not support the hypothesis that this genetic break reflects contemporary geographical isolation. The four distinct clades observed among coastal waters of southern China and Taiwan indicated underestimated diversity. It is noteworthy that the cryptic diversity is vulnerable under high pressure of human activity.     

Cross-Reactions between the Cytotoxic T-Lymphocyte Responses of Human Immunodeficiency Virus-Infected African and European Patients

The great variability of protein sequences from human immunodeficiency virus (HIV) type 1 (HIV-1) isolates represents a major obstacle to the development of an effective vaccine against this virus. The surface protein (Env), which is the predominant target of neutralizing antibodies, is particularly variable. Here we examine the impact of variability among different HIV-1 subtypes (clades) on cytotoxic T-lymphocyte (CTL) activities, the other major component of the antiviral immune response. CTLs are produced not only against Env but also against other structural proteins, as well as some regulatory proteins. The genetic subtypes of HIV-1 were determined for Env and Gag from several patients infected either in France or in Africa. The cross-reactivities of the CTLs were tested with target cells expressing selected proteins from HIV-1 isolates of clade A or B or from HIV type 2 isolates. All African patients were infected with viruses belonging to clade A for Env and for Gag, except for one patient who was infected with a clade A Env-clade G Gag recombinant virus. All patients infected in France were infected with clade B viruses. The CTL responses obtained from all the African and all the French individuals tested showed frequent cross-reactions with proteins of the heterologous clade. Epitopes conserved between the viruses of clades A and B appeared especially frequent in Gag p24, Gag p18, integrase, and the central region of Nef. Cross-reactivity also existed among Gag epitopes of clades A, B, and G, as shown by the results for the patient infected with the clade A Env-clade G Gag recombinant virus. These results show that CTLs raised against viral antigens from different clades are able to cross-react, emphasizing the possibility of obtaining cross-immunizations for this part of the immune response in vaccinated individuals.     

Geographic variation and diversity of the cytochrome b gene in wild populations of medaka (Oryzias latipes) from Korea and China

We analyzed the polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLPs) of the mitochondrial cytochrome b (cyt b) gene in wild populations of medaka from Korea and China. We surveyed 258 wild specimens from 75 different sites, and identified 17 mitotypes. Sequencing analysis of the complete cyt b gene (1141-bp) was subsequently carried out to infer the phylogenetic relationships among these mitotypes. Phylogenetic trees indicated two major clades, D and E, which were different from the Japanese clades (A, B and C). These two clades were completely identical to two clusters previously identified by RFLP analysis of entire mitochondrial DNAs. The geographic distribution of the mitotypes in clades D and E was consistent with the China-West Korean Population and the East Korean Population as defined by allozymic and karyological analyses. This agreement among different analyses suggests long-term isolation between the two groups. In the region where the distributions of two major clades overlapped, a limited extent of gene flow was observed. These results suggested the existence of some reproductive isolation mechanisms between the two clades, or the introgression between them followed by a random drift in each local population. Furthermore, clade D was subdivided into three subclades (D-I to D-III). The phylogenetic relationship and distribution pattern of subclade D-II suggested a dispersal event of medaka from China to southwest Korea. Our results also showed that the East Korean Population has recently expanded its distribution area because little diversity was observed in clade E.     

Origin and phylogeography of African savannah elephants (<Emphasis Type="Italic">Loxodonta africana</Emphasis>) in Kruger and nearby parks in southern Africa

African savannah elephants (Loxodonta africana) occur in fragmented and isolated populations across southern Africa. Transfrontier conservation efforts aim at preventing the negative effects of population fragmentation by maintaining and restoring linkages between protected areas. We sought to identify genetic linkages by comparing the elephants in Kruger National Park (South Africa) to populations in nearby countries (Botswana, Mozambique, Zambia and Zimbabwe). We used a 446 base pair mitochondrial DNA (mtDNA) control region fragment (141 individuals) and 9 nuclear DNA (nDNA) microsatellite markers (69 individuals) to investigate phylogenetic relationships and gene flow among elephant populations. The mtDNA and nDNA phylogeographic patterns were incongruent, with mtDNA patterns likely reflecting the effects of ancient female migrations, with patterns persisting due to female philopatry, and nDNA patterns likely reflecting male-mediated dispersal. Kruger elephant heterozygosity and differentiation were examined, and were not consistent with genetic isolation, a depleted gene pool or a strong founder effect. Mitochondrial DNA geographic patterns suggested that the Kruger population was founded by elephants from areas both north and south of Kruger, or has been augmented through migration from more than one geographic source. We discuss our findings in light of the need for conservation initiatives that aim at maintaining or restoring connectivity among populations. Such initiatives may provide a sustainable, self-regulating management approach for elephants in southern Africa while maintaining genetic diversity within and gene flow between Kruger and nearby regions.     

Relationships among cave swallow populations (Petrochelidon fulva) determined by comparisons of microsatellite and cytochrome b data

The cave swallow (Petrochelidon fulva) is a polytypic species with isolated populations in northwestern South America, southwestern North America, Yucatan, Greater Antilles, and Florida. We compared microsatellite genotypes of at least five individuals each from five populations and cytochrome b sequence data of two individuals each from seven populations plus two outgroups. Microsatellite allelic diversity was substantial, and the North American populations were about equally variable. In contrast, the Ecuadorian population had far less genetic variation. Gene flow was apparent among populations, especially between Texas and Florida. Genetic structure was greater than in widespread North American species but less than that of sedentary Neotropical birds. Microsatellite genetic distances indicated a close affinity between Ecuadorian and northern populations, especially Texas and Florida, but this finding was inconsistent with cytochrome b data, which indicated that the Ecuadorian population is the clear outgroup to the northern populations. Its outgroup status is consistent with recent classifications that designate South American populations as their own species (P. rufocollaris). The cytochrome b data further suggested that the northern populations are divided into two clades: Texas/Yucatan and Florida/Greater Antilles. The microsatellite data incorrectly measured the diversity and affinities of Ecuadorian birds apparently because of an ascertainment bias that results from the use of heterologous PCR primers. Despite these problems in measuring phylogenetic relationships, the microsatellite data appeared to work well as a population genetic marker in indicating population structure and gene flow.     

Thaptomys Thomas 1915 (Rodentia, Sigmodontinae, Akodontini) with karyotypes 2n = 50, FN = 48, and 2n = 52, FN = 52: Two monophyletic lineages recovered by molecular phylogeny

A novel karyotype with 2n = 50, FN = 48, was described for specimens of Thaptomys collected at Una, State of Bahia, Brazil, which are morphologically indistinguishable from Thaptomys nigrita, 2n = 52, FN = 52, found in other localities. It was hence proposed that the 2n = 50 karyotype could belong to a distinct species, cryptic of Thaptomys nigrita, once chromosomal rearrangements observed, along with the geographic distance, might represent a reproductive barrier between both forms. Phylogenetic analyses using maximum parsimony and maximum likelihood based on partial cytochrome b sequences with 1077 bp were performed, attempting to establish the relationships among the individuals with distinct karyotypes along the geographic distribution of the genus; the sample comprised 18 karyotyped specimens of Thaptomys, encompassing 15 haplotypes, from eight different localities of the Atlantic Rainforest. The intra-generic relationships corroborated the distinct diploid numbers, once both phylogenetic reconstructions recovered two monophyletic lineages, a northeastern clade grouping the 2n = 50 and a southeastern clade with three subclades, grouping the 2n = 52 karyotype. The sequence divergence observed between their individuals ranged from 1.9% to 3.5%.     

Genetic diversity of free-living Symbiodinium in surface water and sediment of Hawai‘i and Florida

Marine dinoflagellates in the genus Symbiodinium are primarily known for their symbiotic associations with invertebrates and protists, although they are also found free-living in nanoplankton and microphytobenthic communities. Free-living Symbiodinium are necessary for hosts that must acquire their symbionts anew each generation and for the possible reestablishment of endosymbiosis in bleached adults. The diversity and ecology of free-living Symbiodinium are not well studied by comparison with their endosymbiotic counterparts, and as a result, our understanding of the linkages between free-living and endosymbiotic Symbiodinium is poor. Here, we begin to address this knowledge gap by describing the genetic diversity of Symbiodinium in the surface water and reef sediments of Hawai‘i and Florida using Symbiodinium-specific primers for the hypervariable region of the chloroplast 23S domain V (cp23S-HVR). In total, 29 Symbiodinium sequence types were detected, 16 of which were novel. The majority of Symbiodinium sequence types in free-living environments belonged to clades A and B, but smaller numbers of sequence types belonging to clades C, D, and G were also detected. The majority of sequences recovered from Hawai‘i belonged to clades A and C and those from Florida to clade B. Such distribution patterns are consistent with the endosymbiotic diversity previously reported for these two regions. The ancestral sequence types in each clade were typically recovered from surface water and sediments both in Hawai‘i and Florida and have been previously reported as endosymbionts of a range of invertebrates, suggesting that these types have the capacity to exploit a range of very different habitats. More derived sequence types in clades A, B, C, and G were not recovered here, suggesting they are potentially restricted to endosymbiotic environments.