GLOBAL SYSTEMATIC AND PHYLOGENETIC ANALYSIS OF SARGASSUM IN THE GULF OF MEXICO,CARIBBEAN AND PACIFIC BASIN

Sargassum is one of the most species‐rich genera in the brown algae with over 400 described species worldwide. The bulk of these species occurs in Pacific‐Indian ocean waters with only a small portion found on the Atlantic side of the Isthmus of Panama. Sargassum also has one of the most subdivided and complex taxonomic systems used within the algae. Systematic distinctions within the genus are further complicated by high rates of phenotypic variability in several key morphological characters. Molecular analyses in such systems should allow testing of systematic concepts while providing insights into speciation and evolutionary patterns. Global molecular phylogenetic analyses using both conserved and variable regions of the Rubisco operon (rbcL and rbcL‐IGS‐rbcS) were performed with species from the Gulf of Mexico, Caribbean, and Pacific basin. Results confirm earlier analyses based on rbcL‐IGS‐rbcS from Pacific species at the subgeneric and sectional level while providing additional insights into the systematics and phylogenetics on a global scale. For example, species east of the Isthmus of Panama form a distinct well‐resolved clade within the tropical subgenus. This result in sharp contrast to traditional systematic treatments but provides a window into the evolutionary history of this genus in the Pacific and Atlantic Ocean basins and a possible means to time speciation events.     

Historical biogeography and speciation in the reef fish genus Haemulon (Teleostei: Haemulidae)

The high biodiversity of tropical marine hotspots has long intrigued evolutionary biologists and biogeographers. The genus Haemulon (grunts) is one of the most important (numerically, ecologically, and economically) reef fish groups in the New World and an excellent candidate to test hypotheses of speciation and diversity generation in the Greater Caribbean, the richest Atlantic biodiversity hotspot, as well as the eastern Pacific. To elucidate the phylogenetic relationships among the species of Haemulon, we obtained a combined total of 2639 base pairs from two mitochondrial genes (cytochrome b and cytochrome oxidase I), and two nuclear genes (TMO-4C4 and RAG2) from all nominal species. Parsimony, Maximum likelihood, and Bayesian analyses resulted in a well-resolved phylogeny with almost identical topologies. Previous phylogenetic hypotheses based on adult morphology, such as the close relationship among H. aurolineatum, H. boschmae, and H. striatum were not supported, whereas others using developmental characters, such as the relationship between H. plumieri and H. sciurus, were confirmed. Our data also indicate that the populations of the nominal H. steindachneri from the two sides of the Isthmus of Panama are genetically divergent at the species level in each ocean, and that the boga, Inermia vittata (family Inermiidae), belongs in the genus Haemulon. This evidence implies that there are 21 valid species of Haemulon, two more than previously recognized. The Amazon barrier and the Isthmus of Panama seem to have played roles in allopatric speciation of Haemulon. However, the majority of sister species pairs have completely overlapping distributions, indicating that vicariance is not the only process driving speciation in this genus. We conclude that both vicariance between biogeographic provinces, and ecological mechanisms of speciation within provinces contribute to species richness in the genus Haemulon.     

Dispersal barriers in tropical oceans and speciation in Atlantic and eastern Pacific sea urchins of the genus Echinometra

Echinometra is a pantropical sea urchin made famous through studies of phylogeny, speciation, and genetic structure of the Indo-West Pacific (IWP) species. We sequenced 630 bp of the cytochrome oxidase I (COI) mitochondrial gene to provide comparable information on the eastern Pacific and Atlantic species, using divergence between those separated by closure of the Isthmus of Panama 3.1 million years ago (Ma) to estimate dates for cladogenic events. Most recently (1.27-1. 62 Ma), the Atlantic species E. lucunter and E. viridis diverged from each other, at a time in the Pleistocene that sea levels fell and Caribbean coral speciation and extinction rates were high. An earlier split, assumed to have been coincident with the completion of the Isthmus of Panama, separated the eastern Pacific E. vanbrunti from the Atlantic common ancestor. Transisthmian COI divergence similar to that in the sea urchin genus Eucidaris supports this assumption. The most ancient split in Echinometra occurred between the IWP and the neotropical clades, due to cessation of larval exchange around South Africa or across the Eastern Pacific Barrier. Gene flow within species is generally high; however, there are restrictions to genetic exchange between E. lucunter populations from the Caribbean and those from the rest of the Atlantic. Correlation between cladogenic and vicariant events supports E. Mayr's contention that marine species, despite their high dispersal potential, form by means of geographical separation. That sympatric, nonhybridizing E. lucunter and E. viridis were split so recently suggests, however, that perfection of reproductive barriers between marine species with large populations can occur in less than 1.6 million years (Myr).     

Molecular ecology, speciation, and evolution of the reef fish genus Anisotremus

Grunts (family Haemulidae) in the genus Anisotremus comprise 10 described species which occur predominantly on coral reefs and subtropical rocky reefs in the Neotropics of the Tropical Eastern Pacific the Caribbean and adjacent waters. In this study, the phylogenetic relationships for all described species were examined based on one mitochondrial gene (cytochrome b) and one nuclear marker (the first intron of the ribosomal protein S7). Closely related species of the genus Haemulon and the single representative of the genus Genyatremus, G. luteus were also included in the analysis, following the suggestion, based on morphological data, that they may be closely related to, or possibly placed within, Anisotremus. Two sweetlips, genus Plectorhinchus, which belong to the recognized sister subfamily Plectorhynchinae, were used as outgroups. Two species pairs in the ingroup genus Anisotremus are geminate species, which presumably diverged after the rise of the Isthmus of Panama, thus providing an internal molecular clock calibration. This allowed for a comprehensive evolutionary scenario for the genus. Our data were consistent with two independent allopatric speciation events (geminate species), and one likely sympatric speciation event. Our data were also consistent with the placement of Genyatremus and Haemulon within the genus Anisotremus, thus breaking its monophyletic status. As proposed for other coral reef species, Anisotremus seems to have colonized coral reefs from non-coral reef habitats. In addition, ancestral species seem to have been widespread, since species that are currently found in Brazilian and Pacific waters are basal on the phylogenetic tree. Finally, this study adds to the hypothesis of a secondary evolutionary center in the New World.     

Phylogeography of Ophioblennius: the role of ocean currents and geography in reef fish evolution

Many tropical reef fishes are divided into Atlantic and East Pacific taxa, placing similar species in two very different biogeographic regimes. The tropical Atlantic is a closed ocean basin with relatively stable currents, whereas the East Pacific is an open basin with unstable oceanic circulation. To assess how evolutionary processes are influenced by these differences in oceanography and geography, we analyze a 630-bp region of mitochondrial cytochrome b from 171 individuals in the blenniid genus Ophioblennius. Our results demonstrate deep genetic structuring in the Atlantic species, O. atlanticus, corresponding to recognized biogeographic provinces, with divergences of d = 5.2-12.7% among the Caribbean, Brazilian, St. Helena/Ascension Island, Gulf of Guinea, and Azores/Cape Verde regions. The Atlantic phylogeny is consistent with Pliocene dispersal from the western to eastern Atlantic, and the depth of these separations (along with prior morphological comparisons) may indicate previously unrecognized species. The eastern Pacific species, O. steindachneri, is characterized by markedly less structure than O. atlanticus, with shallow mitochondrial DNA lineages (dmax = 2.7%) and haplotype frequency shifts between locations in the Sea of Cortez, Pacific Panama, Clipperton Island, and the Galapagos Islands. No concordance between genetic structure and biogeographic provinces was found for O. steincdachneri. We attribute the phylogeographic pattern in O. atlanticus to dispersal during the reorganization of Atlantic circulation patterns that accompanied the shoaling of the Isthmus of Panama. The low degree of structure in the eastern Pacific is probably due to unstable circulation and linkage to the larger Pacific Ocean basin. The contrast in genetic signatures between Atlantic and eastern Pacific blennies demonstrates how differences in geology and oceanography have influenced evolutionary radiations within each region.     

Extreme gender flexibility: using a phylogenetic framework to infer the evolution of variation in sex allocation, phylogeography, and speciation in a genus of bidirectional sex changing fishes(Lythrypnus, Gobiidae)

The genus Lythrypnus is a group of marine gobies that exhibit extreme gender flexibility as bidirectional sex changers. The genus consists of 20 described species and several undescribed species that are distributed in the Americas. Five species have been characterized with respect to sex allocation and gonad morphology. The hormonal, morphological, and behavioral aspects of sex change have been studied extensively for one species, L. dalli. These data, however, have not been interpreted in an evolutionary context because a phylogenetic hypothesis has not previously been proposed for the genus Lythrypnus. We propose the first phylogenetic hypothesis for the genus based on molecular data from three mitochondrial genes (12s, ND2, and Cytb), one nuclear gene (Rag1) and one nuclear intron (S7). We also include three previously undescribed Lythrypnus species. Our results support the monophyly of the genus with L. heterochroma, an Atlantic species, as the basal taxon. After the divergence of L. heterochroma, there are two main clades, one comprised of species distributed in the Atlantic, the other comprised of species distributed in the Pacific. These data indicate an Atlantic origin for the genus, followed by divergence after the closure of the Isthmus of Panama. Our data also support the monophyly of three previously described species complexes, the L. rhizophora complex and L. dalli complex in the Pacific, and the L. mowbrayi complex in the Atlantic. We mapped patterns of sex allocation within this genus onto the fully resolved and supported topology, and found that sexual plasticity and gender flexibility is likely a synapomorphy for the genus. Overall our results create a well-supported framework to understand the phylogeography of the genus, and to interpret the evolution of sex allocation in Lythrypnus gobies.     

Phylogeny of the genus Merluccius based on mitochondrial and nuclear genes

Genus Merluccius is considered one of the most important groups within the Teleostei, and comprises 12 extant species distributed along the coasts of America, Europe and Africa, being its fisheries very important in these continents. Despite their noticeable economical importance for humans, to date the phylogeny of hakes has not been clearly established. In this study we used mitochondrial sequences (the ribosomal genes 12S rDNA and 16S rDNA, the coding gene cytochrome b and the control region) and the nuclear 5S rDNA conserved region in order to determine the phylogenetic and biogeographical relationships within the genus Merluccius. This is the first time that all the species of this genus recognized by the FAO are included in a phylogeny. Maximum Parsimony, Maximum Likelihood and Bayesian analyses of the mitochondrial sequences suggest that the geographical origin of the genus was the North Atlantic Ocean, and indicate that two main clades, early separated in the evolution, exist within the genus: one American (7 species) and one Euro-African (5 species). Among the American species, M. bilinearis seems to be the most ancient one, and the rise of the Panama Isthmus could act as a physical barrier leading to further processes of speciation. Within the Euro-African clade, successive events of geographical differentiation could explain the observed pattern of species distribution. Therefore, we propose both vicariant speciation and geographical dispersion as main mechanisms to explain the evolutionary history of the genus Merluccius.     

PHYLOGEOGRAPHY OF THE PANTROPICAL SEA URCHIN EUCIDARIS IN RELATION TO LAND BARRIERS AND OCEAN CURRENTS

The pantropical sea urchin genus Eucidaris contains four currently recognized species, all of them allopatric: E. metularia in the Indo-West Pacific, E. thouarsi in the eastern Pacific, E. tribuloides in both the western and eastern Atlantic, and E. clavata at the central Atlantic islands of Ascension and St. Helena. We sequenced a 640-bp region of the cytochrome oxidase I (COI) gene of mitochondrial DNA to determine whether this division of the genus into species was confirmed by molecular markers, to ascertain their phylogenetic relations, and to reconstruct the history of possible dispersal and vicariance events that led to present-day patterns of species distribution. We found that E. metularia split first from the rest of the extant species of the genus. If COI divergence is calibrated by the emergence of the Isthmus of Panama, the estimated date of the separation of the Indo-West Pacific species is 4.7–6.4 million years ago. This date suggests that the last available route of genetic contact between the Indo-Pacific and the rest of the tropics was from west to east through the Eastern Pacific Barrier, rather than through the Tethyan Sea or around the southern tip of Africa. The second cladogenic event was the separation of eastern Pacific and Atlantic populations by the Isthmus of Panama. Eucidaris at the outer eastern Pacific islands (Galapagos, Isla del Coco, Clipperton Atoll) belong to a separate clade, so distinct from mainland E. thouarsi as to suggest that this is a different species, for which the name E. galapagensis is revived from the older taxonomic literature. Complete lack of shared alleles in three allozyme loci between island and mainland populations support their separate specific status. Eucidaris galapagensis and E. thouarsi are estimated from their COI divergence to have split at about the same time that E. thouarsi and E. tribuloides were being separated by the Isthmus of Panama. Even though currents could easily convey larvae between the eastern Pacific islands and the American mainland, the two species do not appear to have invaded each other's ranges. Conversely, the central Atlantic E. clavata at St. Helena and Ascension is genetically similar to E. tribuloides from the American and African coasts. Populations on these islands are either genetically connected to the coasts of the Atlantic or have been colonized by extant mitochondrial DNA lineages of Eucidaris within the last 200,000 years. Although it is hard to explain how larvae can cross the entire width of the Atlantic within their competent lifetimes, COI sequences of Eucidaris from the west coast of Africa are very similar to those of E. tribuloides from the Caribbean. F_ST statistics indicate that gene flow between E. metularia from the Indian Ocean and from the western and central Pacific is restricted. Low gene flow is also evident between populations of E. clavata from Ascension and St. Helena. Rates of intraspecific exchange of genes in E. thouarsi, E. galapagensis, and E. tribuloides, on the other hand, are high. The phylogeny of Eucidaris confirms Ernst Mayr's conclusions that major barriers to the dispersal of tropical echinoids have been the wide stretch of deep water between central and eastern Pacific, the cold water off the southwest coast of Africa, and the Isthmus of Panama. It also suggests that a colonization event in the eastern Pacific has led to speciation between mainland and island populations.     

Speciation and diversity on tropical rocky shores: a global phylogeny of snails of the genus Echinolittorina

A phylogenetic approach to the origin and maintenance of species diversity ideally requires the sampling of all species within a clade, confirmation that they are evolutionarily distinct entities, and knowledge of their geographical distributions. In the marine tropics such studies have mostly been of fish and reef-associated organisms, usually with high dispersal. In contrast, snails of the genus Echinolittorina (Littorinidae) are restricted to rocky shores, have a four-week pelagic development (and recorded dispersal up to 1400 km), and show different evolutionary patterns. We present a complete molecular phylogeny of Echinolittorina, derived from Bayesian analysis of sequences from nuclear 28S rRNA and mitochondrial 12S rRNA and COI genes (nodal support indicated by posterior probabilities, maximum likelihood, and neighbor-joining bootstrap). This consists of 59 evolutionarily significant units (ESUs), including all 50 known taxonomic species. The 26 ESUs found in the Indo-West Pacific region form a single clade, whereas the eastern Pacific and Atlantic species are basal. The earliest fossil occurred in the Tethys during the middle Eocene and we suggest that the Indo-West Pacific clade has been isolated since closure of the Tethyan seaway in the early Miocene. The geographical distributions of all species (based on more than 3700 locality records) appear to be circumscribed by barriers of low temperature, unsuitable sedimentary habitat, stretches of open water exceeding about 1400 km, and differences in oceanographic conditions on the continuum between oceanic and continental. The geographical ranges of sister species show little or no overlap, indicating that the speciation mode is predominantly allopatric. Furthermore, range expansion following speciation appears to have been limited, because a high degree of allopatry is maintained through three to five branching points of the phylogeny. This may be explained by infrequent long-distance colonization, habitat specialization on the oceanic/continental gradient, and perhaps by interspecific competition. In the eastern Pacific plus Atlantic we identify five cases of divergence on either side of the Isthmus of Panama, but our estimates of their ages pre-date the emergence of the Isthmus. There are three examples of sister relationships between species in the western Atlantic and eastern Atlantic, all resulting from dispersal to the east. Within the Indo-West Pacific, we find no geographical pattern of speciation events; narrowly endemic species of recent origin are present in both peripheral and central parts of the region. Evidence from estimated divergence times of sister species, and from a plot of the number of lineages over time, suggest that there has been no acceleration of diversification during the glacio-eustatic cycles of the Plio-Pleistocene. In comparison with reefal organisms, species of Echinolittorina on rocky shores may be less susceptible to extinction or isolation during sea-level fluctuations. The species richness of Echinolittorina in the classical biogeographic provinces conforms to the common pattern of highest diversity (11 species) in the central "East Indies Triangle" of the Indo-West Pacific, with a subsidiary focus in the eastern Pacific and western Atlantic, and lowest diversity in the eastern Atlantic. The diversity focus in the East Indies Triangle is produced by a mosaic of restricted allopatric species and overlap of a few widespread ones, and is the result of habitat specialization rather than historical vicariance. This study emphasizes the plurality of biogeographic histories and speciation patterns in the marine tropics.     

Tethyan vicariance, relictualism and speciation: evidence from a global molecular phylogeny of the opisthobranch genus Bulla

Aim Our aims were: (1) to reconstruct a molecular phylogeny of the cephalaspidean opisthobranch genus Bulla, an inhabitant of shallow sedimentary environments; (2) to test if divergence times are consistent with Miocene and later vicariance among the four tropical marine biogeographical provinces; (3) to examine the phylogenetic status of possible Tethyan relict species; and (4) to infer the timing and causes of speciation events. Location Tropical and warm‐temperate regions of the Atlantic, Indo‐West Pacific, Australasia and eastern Pacific. Methods Ten of the 12 nominal species of Bulla were sampled, in a total sample of 65 individuals, together with cephalaspidean outgroups. Phylogenetic relationships were inferred by Bayesian analysis of partial sequences of the mitochondrial cytochrome c oxidase I (COI) and 16S rRNA and nuclear 28S rRNA genes. Divergence times and rates of evolution were estimated using uncorrelated relaxed‐clock Bayesian methods with fossil calibrations (based on literature review and examination of fossil specimens), implemented in beast . The geographical pattern of speciation was assessed by estimating the degree of overlap between sister lineages. Results Four clades were supported: Indo‐West Pacific (four species), Australasia (one species), Atlantic plus eastern Pacific (three species) and Atlantic (two species), with estimated mean ages of 35–46 Ma. Nominal species were monophyletic, but deep divergences were found within one Indo‐West Pacific and one West Atlantic species. Species‐level divergences occurred in the Miocene or earlier. The age of a sister relationship across the Isthmus of Panama was estimated at 7.9–32.1 Ma, and the divergence of a pair of sister species on either side of the Atlantic Ocean occurred 20.4–27.2 Ma. Main conclusions Fossils suggest that Bulla originated in the Tethys realm during the Middle Eocene. Average ages of the four main clades fall in the Eocene, and far pre‐date the 18–19 Ma closure of the Tethys Seaway. This discrepancy could indicate earlier vicariant events, selective extinction or errors of calibration. Similarly, the transisthmian divergence estimate far pre‐dates the uplift of the Panamanian Isthmus at about 3 Ma. Speciation events occurred in the Miocene, consistent with tectonic events in the central Indo‐West Pacific, isolation of the Arabian Sea by upwelling and westward trans‐Atlantic dispersal. Differences in habitat between sister species suggest that ecological speciation may also have played a role. The basal position of the Australasian species supports its interpretation as a Tethyan relict.     

PHYLOGENETIC RELATIONSHIPS OF GELIDIALES SPECIES IN COSTA RICA

Despite a general paucity of studies on marine algae in Costa Rica, within the red algal order Gelidiales, 9 species are reported from the Caribbean, and 6 species from the Pacific. In this study 5 species from the southeast Caribbean coast and 2 species from the northwest Pacific coast of Costa Rica were collected for DNA sequence and morphological analyses. At the time of this writing, morphological observations of four Caribbean taxa have identified them as Gelidium microdonticum , Pterocladiella capillacea , P. melanoidea , and Gelidiella acerosa. In rbc L sequence analyses, Gelidium microdonticum is resolved within a clade of small Gelidium species predominantly found in the south Atlantic. Two collections representing different forms of Pterocladiella melanoidea sensu Dawson were found to have identical rbc L sequences. These samples were resolved in rbc L trees with a taxon from Texas identified as P. bartlettii and not P. melanoidea from Europe. Comparisons with type material are being made to verify these identifications so that the status of P. melanoidea in the Caribbean may be determined. The unidentified Caribbean taxon is resolved as a distinct species within the Pterocladiella clade as well. Gelidiella acerosa from Caribbean Costa Rica is closely allied with other Caribbean G. acerosa samples in rbc L trees. The two pacific taxa are small intertidal turf species and have not yet been identified. Sequence analyses resolve these taxa within a large clade of Indo-Pacific and Caribbean Gelidium species.     

PHYLOGEOGRAPHY OF THE TRUMPETFISHES (AULOSTOMUS): RING SPECIES COMPLEX ON A GLOBAL SCALE

Abstract.— The distribution of circumtropical marine species is limited by continental boundaries, cold temperate conditions, and oceanic expanses, but some of these barriers are permeable over evolutionary time scales. Sister taxa that evolved in separate ocean basins can come back into contact, and the consequences of this renewed sympatry may be a key to understanding evolutionary processes in marine organisms. The circumtropical trumpetfishes (Aulostomus) include a West Atlantic species (A. maculatus), an Indian‐Pacific species (A. chinensis), and an East Atlantic species (A. strigosus) that may be the product of a recent invasion from the Indian Ocean. To resolve patterns of divergence and speciation, we surveyed 480 bp of mitochondrial DNA cytochrome b in 196 individuals from 16 locations. Based on a conventional molecular clock of 2% sequence divergence per million years, the deepest partitions in a neighbor‐joining tree (d= 0.063‐0.082) are consistent with separation of West Atlantic and Indian‐Pacific species by the Isthmus of Panama, 3–4 million years ago. By the same criteria, trumpetfish in the East Atlantic were isolated from the Indian Ocean about 2.5 million years ago (d= 0.044‐0.054), coincident with the advent of glacial cycles and cold‐water upwelling around South Africa. Continental barriers between tropical oceans have only rarely been surmounted by trumpetfishes, but oceanic barriers do not appear to be substantial, as indicated by weak population partitioning (ø_ST= 0.093) in A. chinensis across the Indian and Pacific Oceans. Finally, morphological and mitochondrial DNA data indicate hybridization of A. strigosus and A. maculatus in Brazil. After 3–4 million years and a globe‐spanning series of vicariant and dispersal events, trumpetfish lineages have come back into contact in the southwest Atlantic and appear to be merging. This ring species phenomenon may occur in a broad array of marine organisms, with clear implications for the production and maintenance of biodiversity in marine ecosystems.     

Phylogeography of the Calonectris shearwaters using molecular and morphometric data

We investigated phylogenetic relationships and the biogeographic history of the Calonectris species complex, using both molecular and biometric data from one population of the Cape Verde shearwater Calonectris edwardsii (Cape Verde Islands), one from the streaked shearwater C. leucomelas (western Pacific Ocean) and 26 from Cory's shearwater populations distributed across the Atlantic (C. d. borealis) and the Mediterranean (C. d. diomedea). The streaked shearwater appeared as the most basal and distant clades, whereas the genetic divergences among the three main clades within the Palearctic were similar. Clock calibrations match the first speciation event within Calonectris to the Panama Isthmus formation, suggesting a vicariant scenario for the divergence of the Pacific and the Palearctic clades. The separation between the Atlantic and Mediterranean clades would have occurred in allopatry by range contraction followed by local adaptation during the major biogeographic events of the Pleistocene. The endemic form from Cape Verde probably evolved as a result of ecological divergence from the Mediterranean subspecies. Finally, one Mediterranean population (Almeria) was unexpectedly grouped into the Atlantic subspecies clade, both by genetic and by morphometric analyses, pointing out the Almeria-Oran oceanographic front (AOOF) as the actual divide between the two Cory's shearwater subspecies. Our results highlight the importance of oceanographic boundaries as potentially effective barriers shaping population and species phylogeographical structure in pelagic seabirds.     

Molecular phylogeny reveals extensive ancient and ongoing radiations in a snapping shrimp species complex (Crustacea,Alpheidae, Alpheus armillatus)

Tropical marine habitats often harbor high biodiversity, including many cryptic taxa. Though the prevalence of cryptic marine taxa is well known, the evolutionary histories of these groups remain poorly understood. The snapping shrimp genus Alpheus is a good model for such investigations, as cryptic species complexes are very common, indicating widespread genetic diversification with little or no morphological change. Here, we present an extensive phylogeographic investigation of the diversified amphi-American Alpheus armillatus species complex, with geographic sampling in the Caribbean Sea, Gulf of Mexico, Florida, Brazil, and the tropical Eastern Pacific. Sequence data from two mitochondrial genes (16SrRNA and cytochrome oxidase I) and one nuclear gene (myosin heavy chain) provide strong evidence for division of the species complex into six major clades, with extensive substructure within each clade. Our total data set suggests that the A. armillatus complex includes no less than 19 putative divergent lineages, 11 in the Western Atlantic and 8 in the Eastern Pacific. Estimates of divergence times from Bayesian analyses indicate that the radiation of the species complex began ～10 MYA with the most recent divergences among subclades dating to within the last 3 MY. Furthermore, individuals from the six major clades had broadly overlapping geographic distributions, which may reflect secondary contact among previously isolated lineages, and have apparently undergone several changes in superficial coloration, which is typically the most pronounced phenotypic character distinguishing lineages. In addition, the extensive substructure within clades indicates a great deal of molecular diversification following the rise of the Isthmus of Panama. In summary, this investigation reflects substantial biodiversity concealed by morphological similarity, and suggests that both ancient and ongoing divergences have contributed to the generation of this biodiversity. It also underlines the necessity to work with the most complete data set possible, which includes comprehensive and wide-ranging sampling of taxa.     

Evolution, biogeography, and the utility of mitochondrial 16s and COI genes in phylogenetic analysis of the crab genus Austinixa (Decapoda: Pinnotheridae)

This study used molecular data (mitochondrial 16s and COI) for the first time to explore evolutionary relationships among species of the pinnotherid crab genus Austinixa. Low levels of phylogenetic signal were detected for COI. High levels of phylogenetic signal were detected for 16s, indicating it is a more useful marker for inferring species level phylogenies in Austinixa. Phylogeographic patterns among species of Austinixa are consistent with allopatric speciation due to numerous climatic and oceanographic fluctuations during the last 5-6 my. In addition, all but two species have been derived since the closure of the Isthmus of Panama, a pattern consistent with hypotheses that the marine biota of the Caribbean and southeastern North America underwent a pulse of biotic turnover within the last 2-3 my. Austinixa aidae and Austinixa hardyi had identical 16s sequences, and differed by only 2 bp in COI, raising questions about the validity of A. hardyi as a distinct species.     

Reconciling molecules and morphology: molecular systematics and biogeography of Neotropical blennies (Acanthemblemaria)

Neotropical reef fish communities are species-poor compared to those of the Indo-West Pacific. An exception to that pattern is the blenny clade Chaenopsidae, one of only three rocky and coral reef fish families largely endemic to the Neotropics. Within the chaenopsids, the genus Acanthemblemaria is the most species-rich and is characterized by elaborate spinous processes on the skull. Here we construct a species tree using five nuclear markers and compare the results to those from Bayesian and parsimony phylogenetic analyses of 60 morphological characters. The sequence-based species tree conflicted with the morphological phylogenies for Acanthemblemaria, primarily due to the convergence of a suite of characters describing the distribution of spines on the head. However, we were able to resolve some of these conflicts by performing phylogenetic analyses on suites of characters not associated with head spines. By using the species tree as a guide, we used a quantitative method to identify suites of correlated morphological characters that, together, produce the distinctive skull phenotypes found in these fishes. A time calibrated phylogeny with nearly complete taxon sampling provided divergence time estimates that recovered a mid-Miocene origin for the genus, with a temporally and geographically complex pattern of speciation both before and after the closure of the Isthmus of Panama. Some sister taxa are broadly sympatric, but many occur in allopatry. The ability to infer the geography of speciation in Acanthemblemaria is complicated by extinctions, incomplete knowledge of their present geographic ranges and by wide-spread taxa that likely represent cryptic species complexes.     

Molecular phylogeny of shrimps from the genus Lysmata (Caridea: Hippolytidae): the evolutionary origins of protandric simultaneous hermaphroditism and social monogamy

Shrimps from the genus Lysmata are known because of their wide diversity of lifestyles, mating systems, symbiotic partnerships, and conspicuous coloration. They can occur in crowds (large aggregations), in small groups, or as socially monogamous pairs. Shrimps from this genus are rare, if not unique among crustaceans, because of their unusual sexual system. To date, the sexual system of all species investigated comprises a protandric simultaneous hermaphroditism: shrimps initially mature and reproduce as males and later in life turn into functional simultaneous hermaphrodites. The evolutionary relationships of the species within the genus are unsettled. A molecular phylogeny of the group may shed light on the evolutionary origins of the peculiar sexual and social systems of these shrimps and help resolve standing taxonomic questions long overdue. Using a 647-bp alignment of the 16S rRNA mitochondrial DNA, we examined the phylogenetic relationship of 21 species of shrimps from the genus Lysmata from several biogeographical regions; the Atlantic, Pacific, and Indo-Pacific. The resulting phylogeny indicates that the genus is paraphyletic and includes the genus Exhippolysmata . The constituent species are subdivided into three well supported clades: one group exclusively composed of neotropical species; a second clade comprising the Indo-Pacific and Atlantic symbiotic fish cleaner shrimps; and a third clade including tropical and temperate species from the Atlantic and Pacific. The molecular phylogeny presented here does not support a historical contingency hypothesis, previously proposed to explain the origins of protandric simultaneous hermaphroditism within the genus. Furthermore, the present study shows that monogamous pair-living is restricted to one monophyletic group of shrimps and therefore probably evolved only once.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 415–424.     

Reconstruction of phylogenetic relationships within Grapsidae (Crustacea: Brachyura) and comparison of trans-isthmian versus amphi-atlantic gene flow based on mtDNA

Following taxonomic revisions in recent years, the originally large family Grapsidae MacLeay, 1838 has become a relatively small and morphologically homogeneous family in terms of adult and larval morphology. Most available molecular studies including more than one genus of the family have also suggested monophyly of the corresponding taxa. However, no single phylogenetic study has ever included all constituent genera of the Grapsidae. In the current study, a molecular phylogeny based on sequences of the mitochondrial 16S rRNA gene from all eight grapsid genera and 34 species is presented and suggests that up to four genera are not monophyletic. This is mainly due to the polyphyletic nature of the genus Pachygrapsus which can be found in six different lineages of the phylogeny, suggesting that the genus currently does not represent a single evolutionary lineage and is in need of taxonomic revision. Amphi-atlantic and trans-isthmian species pairs or populations in four genera are compared and reveal relatively constant and pronounced divergences across the Panama Isthmus as opposed to moderate divergences across the Atlantic Ocean, thereby suggesting occurrence of gene flow across the Atlantic Ocean during the past three million years.     

Marine species formation along the rise of Central America: The anomuran crab Megalobrachium

The evolution of marine neotropical shallow water species is expected to have been greatly affected by physical events related to the emergence of the Central American Isthmus. The anomuran crab Megalobrachium, a strictly neotropical porcellanid genus, consists of four species in the West Atlantic (WA) and nine in the East Pacific (EP). Dispersal is limited to a relatively short planktonic phase, which lasts approximately two weeks. We obtained DNA sequences of three mitochondrial and two nuclear genes of all but one species of Megalobrachium to construct a time‐calibrated phylogeny of the genus and its historical phylogeography, based on the reconstruction of ancestral areas. The topology of the phylogenetic trees of Megalobrachium produced by Bayesian Inference (BI) and Maximum Likelihood (ML) were virtually congruent. The genus is monophyletic with respect to other porcellanids. Ancestral area reconstruction indicates that it arose in the eastern Pacific 18 million years ago and diversified into at least 13 species that are currently formally recognized and three additional species indicated by our data. Most morphological variation appears to have followed phylogenetic differentiation, though some cryptic speciation has also occurred. Four geminate clades in this genus implicate the gradual emergence of the Central American Isthmus in this diversification, but events preceding the final separation of the oceans as well as within‐ocean events after the cessation of water connections were also important.     

Predominant east to west colonizations across major oceanic barriers: Insights into the phylogeographic history of the hydroid superfamily Plumularioidea,suggested by a mitochondrial DNA barcoding marker

We provide preliminary insights into the global phylogeographic and evolutionary patterns across species of the hydrozoan superfamily Plumularioidea (Cnidaria: Hydrozoa). We analyzed 1,114 16S sequences of 198 putative species of Plumularioidea collected worldwide. We investigated genetic connections and divergence in relation to present‐day and ancient biogeographic barriers, climate changes and oceanic circulation. Geographical distributions of most species are generally more constrained than previously assumed. Some species able to raft are dispersed widely. Human‐mediated dispersal explains some wide geographical ranges. Trans‐Atlantic genetic connections are presently unlikely for most of the tropical‐temperate species, but were probably more frequent until the Miocene–Pliocene transition, before restriction of the Tethys Sea and the Central American Seaway. Trans‐Atlantic colonizations were predominantly directed westwards through (sub)tropical waters. The Azores were colonized multiple times and through different routes, mainly from the east Atlantic, at least since the Pliocene. Extant geminate clades separated by the Isthmus of Panama have predominantly Atlantic origin. Various ancient colonizations mainly directed from the Indian Ocean to the Atlantic occurred through the Tethys Sea and around South Africa in periods of lower intensity of the Benguela upwelling. Thermal tolerance, population sizes, dispersal strategies, oceanic currents, substrate preference, and land barriers are important factors for dispersal and speciation of marine hydroids.