Evolutionary history and adaptive significance of respiratory structures on the legs of intertidal porcelain crabs, genus Petrolisthes

Semiterrestrial and terrestrial crabs have evolved multiple strategies for aerial respiration. An uncommon strategy for aerial respiration is seen in porcelain crabs, genus Petrolisthes, where decalcified areas on the meral segments of the walking legs are used as respiratory structures. Here, the evolutionary history and adaptive significance of these structures in porcelain crabs is examined. Interspecific variation in leg membrane size is from 0% to 60% of the surface area of the meral segment. Leg membrane relative size is positively correlated with body size across species but not within one species, Petrolisthes cinctipes. Phylogenetic analyses suggest that leg membranes are ancestral to one of two eastern Pacific Petrolisthes clades. Comparative analyses using phylogenetic independent contrasts indicate a relationship between leg membrane relative size and body size that is phylogenetically independent. In large-bodied intertidal species, whole-animal lactate accumulation during aerial incubation is 200%-300% higher when the leg membranes are obscured, indicating that the leg membranes are functional respiratory structures in these species. Thus, it is possible that leg membranes have facilitated the evolution of larger body sizes by providing additional respiratory surfaces to accommodate the associated higher metabolic demands.     

Phylogenetic relationships of the southern African freshwater crab fauna (Decapoda: Potamonautidae: Potamonautes) derived from multiple data sets reveal biogeographic patterning

The phylogenetic relationships among the southern African freshwater crab species were examined using partial sequence data from three mitochondrial genes (12S rRNA, 16S rRNA, and mtDNA COI) 26 morphological characters and 14 allozyme loci. The aims of the present study were firstly to determine whether freshwater crab species that live in the same geographic region share a close phylogenetic relationship. Secondly, to investigate whether hybridizing species are genetically closely related and thirdly, to test for the validity of subgenera based on the genetic data sets. Phylogenetic analysis based on sequence data revealed largely congruent tree topologies and some associations had consistently high bootstrap support, and these data did not support Bott's subgeneric divisions. The morphological data were less informative for phylogenetic reconstruction while the allozyme data generally supported patterns recovered by the sequence data. A combined analysis of all the data recovered two monophyletic clades, one comprised of small-bodied mountain stream species and the other clade consisting of large-bodied riverine species. The combined analyses reflected clear biogeographic patterning for these river crabs. In addition, there was a clear correlation between genetic distance values and the ability of sympatric species to hybridize.     

Evolutionary diversification of spiny rats (genus Trinomys, Rodentia: Echimyidae) in the Atlantic Forest of Brazil

Phylogenetic and phylogeographic relationships within and among species of the Atlantic Forest spiny rat Trinomys (family Echimyidae) were examined using cytochrome b sequence data. Levels of sequence divergence among species of Trinomys are as high as those found among taxa of echimyids that are recognized as different genera. Trinomys contains three distinct monophyletic clades that show a striking concordance with vegetational distribution. Haplotypes of clade 1 are distributed along the coastal margins of southeastern Brazil, following the moist tropical forest. Members of clade 2 are found in the semi-deciduous tropical forest. T. albispinus represents clade 3 and is found in a more xeric vegetation. Estimates of divergence times separating the three clades are very deep and range from 1.6 to 7.4 millions of years, predating the climatic fluctuations of the Pleistocene. Therefore, the proposed Late Pleistocene refugia in the Atlantic Forest cannot account for the divergence of the clades of Trinomys , but most likely shaped the modern distribution of species. The current taxonomy of this group does not reflect the diversity and phylogenetic relationships of the named species. However, morphological characters are congruent with the phylogeny uncovered by the molecular data. An extensive taxonomic rearrangement is suggested, reflecting phylogenetic relationships of monophyletic entities within the genus Trinomys , degree of sequence differences, and morphological diagnosability.     

Phylogeny of the freshwater crabs of the Western Ghats (Brachyura,Gecarcinucidae)

The Western Ghats mountain range in India is a biodiversity hotspot for a variety of organisms including a large number of endemic freshwater crab species and genera of the family Gecarcinucidae. The phylogenetic relationships of these taxa, however, have remained poorly understood. Here, we present a phylogeny that includes 90% of peninsular Indian genera based on mitochondrial 16S rRNA and nuclear histone H3 gene sequences. The subfamily Gecarcinucinae was found to be paraphyletic with members of two other subfamilies, Liotelphusinae and Parathelphusinae, nesting within. We identify a well‐supported clade consisting of north Indian species and one clade comprising mostly south Indian species that inhabit the southern ‘sky islands’ of the Western Ghats. Relationships of early diverging genera, however, were resolved with low support. This study also includes newly sampled material from an isolated mountain plateau in the northern part of the Western Ghats, representing a new species of Gubernatoriana, which we describe here as Gubernatoriana basalticola sp. n. The new species is immediately distinguished from its congeners and the related genera Ghatiana and Inglethelphusa by its carapace and cheliped morphology, which are unique among Indian freshwater crabs. This study highlights the urgent need for continued faunistic studies to assess the true diversity of gecarcinucid crabs on the Indian subcontinent, to fully understand the basal phylogenetic relationships within the freshwater crab family Gecarcinucidae, and to evaluate the conservation threat status and biogeography of the montane freshwater crabs of the Western Ghats.     

A comparative analysis of the upper thermal tolerance limits of eastern Pacific porcelain crabs, genus Petrolisthes: influences of latitude, vertical zonation, acclimation, and phylogeny

Marine intertidal organisms are subjected to a variety of abiotic stresses, including aerial exposure and wide ranges of temperature. Intertidal species generally have higher thermal tolerance limits than do subtidal species, and tropical species have higher thermal tolerance limits than do temperate species. The adaptive significance of upper thermal tolerance limits of intertidal organisms, however, has not been examined within a comparative context. Here, we present a comparative analysis of the adaptive significance of upper thermal tolerance limits in 20 congeneric species of porcelain crabs, genus Petrolisthes, from intertidal and subtidal habitats throughout the eastern Pacific. Upper thermal tolerance limits are positively correlated with surface water temperatures and with maximal microhabitat temperatures. Analysis of phylogenetically independent contrasts (from a phylogenetic tree on the basis of the 16s rDNA gene sequence) suggests that upper thermal tolerance limits have evolved in response to maximal microhabitat temperatures. Upper thermal tolerance limits increased during thermal acclimation at elevated temperatures, the amount of increase being greater for subtidal than for intertidal species. This result suggests that the upper thermal tolerance limits of some intertidal species may be near current habitat temperature maxima, and global warming thus may affect the distribution limits of intertidal species to a greater extent than for subtidal species.     

Phylogenetic relationships of the ubiquitous coral reef crab subfamily Chlorodiellinae (Decapoda,Brachyura, Xanthidae)

The xanthid subfamily Chlorodiellinae is one of the most ubiquitous coral reef crab taxa in the Indo‐West Pacific region. Many species are common in coral rubble and rocky shores from Hawaii to eastern Africa, often dominating reef cryptofauna in terms of biomass. Phylogenetic analyses of mitochondrial (COX1, 12S rRNA and 16S rRNA) and nuclear (histone H3) gene sequences of 202 specimens indicate that the Chlorodiellinae is polyphyletic as presently defined. Three genera, Pilodius, Cyclodius and Chlorodiella, and two previously undescribed lineages were recovered as a well‐supported clade. In combination with morphological data, the subfamily is redefined and restricted to this clade. Two new genera, Soliella gen. n., and Luniella gen. n., are described based on features of the carapace, male thoracic sternum and male gonopods. The remaining chlorodielline genera and members of the Etisinae, a subfamily with supposedly close morphological affinities to the Chlorodiellinae, were recovered at various positions throughout the xanthid phylogeny, although with relatively low support values. These results reiterate the unresolved status of xanthid subfamilial relationships, but nevertheless provide progress for xanthid systematics.     

Species-level phylogeography and evolutionary history of the hyperdiverse marine gastropod genus Conus

Phylogenetic and paleontological analyses are combined to reveal patterns of species origination and divergence and to define the significance of potential and actual barriers to dispersal in Conus, a species-rich genus of predatory gastropods distributed throughout the world's tropical oceans. Species-level phylogenetic hypotheses are based on nucleotide sequences from the nuclear calmodulin and mitochondrial 16S rRNA genes of 138 Conus species from the Indo-Pacific, eastern Pacific, and Atlantic Ocean regions. Results indicate that extant species descend from two major lineages that diverged at least 33 mya. Their geographic distributions suggest that one clade originated in the Indo-Pacific and the other in the eastern Pacific + western Atlantic. Impediments to dispersal between the western Atlantic and Indian Oceans and the central and eastern Pacific Ocean may have promoted this early separation of Indo-Pacific and eastern Pacific + western Atlantic lineages of Conus. However, because both clades contain both Indo-Pacific and eastern Pacific + western Atlantic species, migrations must have occurred between these regions; at least four migration events took place between regions at different times. In at least three cases, incursions between regions appear to have crossed the East Pacific Barrier. The paleontological record illustrates that distinct sets of Conus species inhabited the Indo-Pacific, eastern Pacific + western Atlantic, and eastern Atlantic + former Tethys Realm in the Tertiary, as is the case today. The ranges of <1% of fossil species (N=841) spanned more than one of these regions throughout the evolutionary history of this group.     

Phylogenetic relationships within Aglaopheniidae (Cnidaria,Hydrozoa) reveal unexpected generic diversity

Morphology can be misleading in the representation of phylogenetic relationships, especially in simple organisms like cnidarians and particularly in hydrozoans. These suspension feeders are widely distributed in many marine ecosystems, and the family Aglaopheniidae Marktanner‐Turneretscher, 1890 is among the most diverse and visible, especially on tropical coral reefs. The taxonomy of this family is based on morphological characters with emphasis on reproductive structures for the identification of genera. This study is the most comprehensive molecular phylogeny of the Aglaopheniidae to date, including six genera and 38 species, of which 13 were investigated for the first time and sampled on tropical coral reefs throughout the Indo‐Pacific region. For newly sampled individuals, we sequenced the 16S rRNA, the nuclear locus comprising the complete ITS1‐5.8S rRNA gene‐ITS2 and the first intron of the calmodulin nuclear gene. Phylogenetic analyses of the data revealed and confirmed a general polyphyly, or doubtful monophyly, of all sampled genera in tropical regions based on both the mitochondrial and nuclear markers. Our results revealed that several morphological characters used today are unsuited to resolve phylogenetic relationships between species and genera, as well as the high phyletic diversity within this family. Future revision of the classification of this family will require extensive geographic sampling and the use of an integrative approach.     

PHYLOGENY AND BIOGEOGRAPHY OF THE ATLANTIC AND EASTERN PACIFIC HYPSELODORIS STIMPSON, 1855 (NUDIBRANCHIA, CHROMODORIDIDAE) WITH THE DESCRIPTION OF A NEW SPECIES FROM THE CARIBBEAN SEA

A new species, based on two specimens from Guana Island, BritishVirgin Islands, is described. The new species agrees with thegenus Hypselodoris in having a high body profile, a large vestibulargland and mantle glands. It differs from other members of thegenus in the Atlantic Ocean by having a reddish background bodycolour. In addition, dorsal colour patterns such as a broadcentral white line with lateral extensions and the lack of yellowlines or spots further differentiate this species. The radularformula of 52x41.0.41 and a smaller seminal receptacle are alsodistinctive. The phylogenetic relationships of 34 species andsubspecies of Hypselodoris from the eastern Pacific and Atlanticare examined using morphological characters. With the exceptionof the new species, these are characterized by a dark blue backgroundbody colour. The phylogenetic analysis of the data matrix resultedin eight most-parsimonious trees. The resulting consensus treeshows that eastern Pacific and Atlantic species of Hypselodorisconstitute a monophyletic group that is basally split into twosister clades. One clade contains the eastern Pacific speciesand most of the Caribbean species, whereas the other clade containsthe eastern Atlantic species. The new species is the sisterto the rest of the Caribbean species, which also form a monophyleticgroup. This phylogenetic hypothesis suggests that two consecutivevicariant events have affected the biogeography of Hypselodoris:(1) the closure of communication between the tropical Indo-Pacificregion and the Atlantic and eastern Pacific, completed withthe formation of the East Pacific Barrier; and (2) the riseof the Panama isthmus. (Received 19 December 2003; accepted 12 October 2005)     

Molecular phylogeny of the Australian frog genera Crinia, Geocrinia, and allied taxa (Anura: Myobatrachidae).

We present a mitochondrial gene tree for representative species of all the genera in the subfamily Myobatrachinae, with special emphasis on Crinia and Geocrinia. This group has been the subject of a number of long-standing taxonomic and phylogenetic debates. Our phylogeny is based on data from approximately 780 bp of 12S rRNA and 676 bp of ND2, and resolves a number of these problems. We confirm that the morphologically highly derived monotypic genera Metacrinia, Myobatrachus, and Arenophryne are closely related, and that Pseudophryne forms the sister group to these genera. Uperoleia and the recently described genus Spicospina are also part of this clade. Our data show that Assa and Geocrinia are reciprocally monophyletic and together they form a well-supported clade. Geocrinia is monophyletic and the phylogenetic relationships with the genus are fully resolved with two major species groups identified: G. leai, G. victoriana, and G. laevis; and G. rosea, G. alba, and G. vitellina (we were unable to sample G. lutea). We confirm that Taudactylus forms the sister group to the other myobatrachine genera, but our data are equivocal on the phylogenetic position of Paracrinia. The phylogenetic relationships among Crinia species are well resolved with strong support for a number of distinct monophyletic clades, but more data are required to resolve relationships among these major Crinia clades. Crinia tasmaniensis and Bryobatrachus nimbus form the sister clade to the rest of Crinia. Due to the lack of generic level synapomorphies for a Bryobatrachus that includes C. tasmaniensis, we synonymize Bryobatrachus with Crinia. Crinia georgiana does not form a clade distinct from other Crinia species and so our data do not support recognition of the genus Ranidella for other Crinia species. Crinia subinsignifera, C. pseudinsignifera, and C. insignifera are extremely closely related despite differences in male advertisement call. A preliminary investigation of phylogeographic substructure within C. signifera revealed significant divergence between samples from across the range of this species.     

Two new species of Phyllonema (Rivulariaceae,Cyanobacteria) with an emendation of the genus

Two untapered, heterocytous species were observed and collected from the intertidal and supratidal zones of the Mexican coastline of the Pacific Ocean near Oaxaca and from the Gulf of Mexico. These populations were highly similar in morphology to the freshwater taxon Petalonema incrustans in the Scytonemataceae. However, 16S rRNA sequence data and phylogenetic analysis indicated that they were sister taxa to the epiphyllic, Brazilian species Phyllonema aveceniicola in the Rivulariaceae, described from culture material. While genetic identity between the two new species was high, they differed significantly in morphology, 16S rRNA gene sequence identity, and sequence and structure of the 16S–23S ITS region. Their morphology differed markedly from the generitype of the previously monotypic Phyllonema, which has tapered, heteropolar, single‐false branched trichomes with very thin or absent sheath. The two new species, Phyllonema ansata and Phyllonema tangolundensis, described from both culture and environmental material, have untapered, isopolar, geminately false branched trichomes with thick, lamellated sheaths, differences so significant that the species would not be placed in Phyllonema without molecular corroboration. The morphological differences are so significant that a formal emendation of the genus is required. These taxa provide a challenge to algal taxonomy because the morphological differences are such that one would logically conclude that they represent different genera, but the phylogenetic evidence for including them all in the same genus is conclusive. This conclusion is counter to the current trend in algal taxonomy in which taxa with minor morphological differences have been repeatedly placed in separate genera based primarily upon DNA sequence evidence.     

Rapid radiation and cryptic speciation in squat lobsters of the genus Munida (Crustacea, Decapoda) and related genera in the South West Pacific: molecular and morphological evidence

Squat lobsters (genus Munida and related genera) are among the most diverse taxa of western Pacific crustaceans, though several features of their biology and phylogenetic relationships are unknown. This paper reports an extensive phylogenetic analysis based on mitochondrial DNA sequences (cytochrome c oxidase subunit I and 16S rRNA) and the morphology of 72 species of 12 genera of western Pacific squat lobsters. Our phylogenetic reconstruction using molecular data supports the recent taxonomic splitting of the genus Munida into several genera. Excluding one species (M. callista), the monophyly of the genus Munida was supported by Bayesian analysis of the molecular data. Three moderately diverse genera (Onconida, Paramunida, and Raymunida) also appeared monophyletic, both according to morphological and molecular data, always with high support. However, other genera (Crosnierita and Agononida) seem to be para- or polyphyletic. Three new cryptic species were identified in the course of this study. It would appear that the evolution of this group was marked by rapid speciation and stasis, or certain constraints, in its morphological evolution.     

Morphological and genetic discordance in two species of Bornean Leptobrachium (Amphibia, Anura, Megophryidae)

Recent phylogenetic studies of Southeast Asian megophryid Leptobrachium, while clarifying (1) distinct specific status of three Philippine populations and (2) high genetic diversities within Bornean Leptobrachium montanum, posed two questions, (1) relationships and divergence histories of two Philippine species and Bornean Leptobrachium gunungense, and (2) possible discordance between phylogenetically and morphologically defined lineages. In order to solve these questions, and especially reviewing current taxonomy of Bornean species, we estimated the phylogenetic relationships of endemic Bornean species together with their putative relatives from Philippines and Sumatra, using 2451 bp sequences of the 12S rRNA, tRNA(val), and 16S rRNA of mitochondrial DNA genes. With respect to Leptobrachium hasseltii and Leptobrachium chapaense, lineages from Borneo, Philippines, and Sumatra formed a monophyletic group with Leptobrachium lumadorum from Mindanao as the basal clade, while two other Philippine species from Palawan and Mindoro formed a clade and nested in Bornean lineages. Sister species relationship of the two Philippine species and L. gunungense is not supported, rejecting the hypothesis of Philippine origin of L. gunungense. Phylogeny does not conform to morphological variation, and the topotypic L. montanum and one lineage of Leptobrachium abbotti are genetically very close despite their clear difference in ventral color pattern. Furthermore, each of these species forms a paraphyletic group and contains several lineages, each of which is a candidate of good species. These results clearly indicate that current taxonomy of Bornean species based on several morphological characteristics requires complete revision. Detailed studies on adult and larval morphology, as well as acoustic characteristics, are necessary to evaluate the taxonomic status of all lineages recovered.     

Identification of Escherichia coli through analysis of 16S rRNA and 16S-23S rRNA internal transcribed spacer region sequences

A bacterial strain, designated BzDS03 was isolated from water sample, collected from Dal Lake Srinagar. The strain was characterized by using 16S ribosomal RNA gene and 16S-23S rRNA internal transcribed spacer region sequences. Phylogenetic analysis showed that 16S rRNA sequence of the isolate formed a monophyletic clade with genera Escherichia. The closest phylogenetic relative was Escherichia coli with 99% 16S rRNA gene sequence similarity. The result of Ribosomal database project's classifier tool revealed that the strain BzDS03 belongs to genera Escherichia.16S rRNA sequence of isolate was deposited in GenBank with accession number FJ961336. Further analysis of 16S-23S rRNA sequence of isolate confirms that the identified strain BzDS03 be assigned as the type strain of Escherichia coli with 98% 16S-23S rRNA sequence similarity. The GenBank accession number allotted for 16S-23S rRNA intergenic spacer sequence of isolate is FJ961337.     

Phylogenetic relationship among horseshoe crab species: effect of substitution models on phylogenetic analyses

The horseshoe crabs, known as living fossils, have maintained their morphology almost unchanged for the past 150 million years. The little morphological differentiation among horseshoe crab lineages has resulted in substantial controversy concerning the phylogenetic relationship among the extant species of horseshoe crabs, especially among the three species in the Indo-Pacific region. Previous studies suggest that the three species constitute a phylogenetically unresolvable trichotomy, the result of a cladogenetic process leading to the formation of all three Indo-Pacific species in a short geological time. Data from two mitochondrial genes (for 16S ribosomal rRNA and cytochrome oxidase subunit I) and one nuclear gene (for coagulogen) in the four species of horseshoe crabs and outgroup species were used in a phylogenetic analysis with various substitution models. All three genes yield the same tree topology, with Tachypleus-gigas and Carcinoscorpius-rotundicauda grouped together as a monophyletic taxon. This topology is significantly better than all the alternatives when evaluated with the RELL (resampling estimated log-likelihood) method.     

New records of two deep-sea eels collected from the Western Pacific Ocean based on COI and 16S rRNA genes

Background

Two deep-sea eels collected from the Western Pacific Ocean are described in this study. Based on their morphological characteristics, the two deep-sea eel specimens were assumed to belong to the cusk-eel family Ophidiidae and the cutthroat eel family Synaphobranchidae.

Methods and results

To accurately identify the species of the deep-sea eel specimens, we sequenced the mitochondrial genes (cytochrome c oxidase subunit I [COI] and 16S ribosomal RNA [16S rRNA]). Through molecular phylogenetic analysis based on mtDNA COI and 16S rRNA gene sequences, these species clustered with the genera Bassozetus and Synaphobranchus, suggesting that the deep-sea eel specimens collected are two species from the genera Bassozetus and Synaphobranchus in the Western Pacific Ocean, respectively.

Conclusions

This is the first study to report new records of the genera Bassozetus and Synaphobranchus from the Western Pacific Ocean based on COI and 16S rRNA genes

     

Phylogenetic relationships of mormyrid electric fishes (Mormyridae; Teleostei) inferred from cytochrome b sequences

The nasute termite genus Nasutitermes is widely distributed over all tropical regions. The phylogenetic relationships among 17 Nasutitermes species from the Pacific tropics were inferred from sequences of mitochondrial cytochrome oxidase II and 16S ribosomal RNA genes. Several methods of analysis yielded phylogenetic trees showing almost the same topology and in good agreement with reconstructions based on morphological or behavioral characters. Neotropical and Australian species came out as separate, apical clades. Asian species split between an apical branch, appearing as sister group to the neotropical clade, and basal taxa. New Guinean species were spread among several clades, suggesting a derivation from multiple origins. A well-supported clade includes the neotropical, Australian, and New Guinean species, with the southeast Asian N. takasagoensis and N. matangensis. It excludes the Asian species N. regularis, N. parvonasutus, and N. longinasus, which might deserve to be removed from Nasutitermes, as well as the long-legged Asian genera Hospitalitermes and Longipeditermes. A Gondwanan origin is proposed for the former clade, although an Old World origin of Nasutitermes followed by dispersal to Australia and South America cannot be excluded.     

PHYLOGENY OF THE DUMONTIACEAE (GIGARTINALES, RHODOPHYTA) AND ASSOCIATED FAMILIES BASED ON SSU rDNA AND INTERNAL TRANSCRIBED SPACER SEQUENCE DATA

Small subunit (SSU) rDNA was sequenced for 25 species in 19 genera of the Gigartinales (Rhodophyta). As well, the internal transcribed spacer (ITS) region was sequenced, and a data matrix of 36 morphological characters was constructed for 16 species of Dumontiaceae. Phylogenetic trees were calculated from a multiple alignment of the SSU sequence data to infer relationships between species of Dumontiaceae and other gigartinalean taxa. The SSU analysis produced a polyphyletic Dumontiaceae. Notably, Acrosymphyton failed to associate with the included Gigartinales, let alone the Dumontiaceae, supporting an earlier proposal to remove it to a new family. The analyses were equivocal about the phylogenetic affinities of Dudresnaya , which clustered with the Kallymeniaceae, and the affinities of the Indo-West Pacific Gibsmithia , Kraftia , and Dasyphloea , the last-mentioned clustering with the Antarctic Gainiaceae, and these four taxa with Portieria (Rhizophyllidaceae). Further investigations are necessary to resolve relationships among these taxa. Rhodopeltis , a genus recently moved to the Dumontiaceae from the Polyideaceae, showed a weak association with the remaining northern Dumontiaceae. The final group consisted of cold-temperate Northern Hemisphere species. Phylogenetic analyses using a combination of SSU, ITS, and morphological data within this clade produced two strongly supported clades, a Dilsea / Neodilsea clade and a Cryptosiphonia / Dumontia clade. Dilsea is derived from a paraphyletic Neodilsea and may itself be polyphyletic. Atlantic and Pacific isolates of Dumontia contorta clearly showed sufficient divergence to warrant recognition as distinct species, and Dumontia alaskana , sp. nov. is proposed for the Pacific species.     

Speciation in the Central American Seaway: the importance of taxon sampling in the identification of trans-isthmian geminate pairs

Aim To create a molecular phylogenetic hypothesis for the closely related serranid genera Alphestes Bloch and Schneider and Dermatolepis Gill and assess the role of the Panamanian Isthmus in speciation within these reef fishes. Location Tropical eastern Pacific, Caribbean, and Indian Oceans. Methods Sequence data from one nuclear (TMO‐4C4) and three mitochondrial genes (16S, 12S, and cytochrome b) were used in maximum parsimony and maximum likelihood analyses. Results Here we show that previously hypothesized trans‐isthmian geminate species are not each other's closest living relatives. Species of Alphestes Bloch and Schneider in the eastern Pacific are sister taxa indicating post‐closure speciation. Within Dermatolepis Gill, we identify a sister group relationship between the Caribbean and western Indian Ocean species, a rarely reported biogeographic pattern. Based on sequence divergence, speciation among the three species of Dermatolepis was, however, nearly simultaneous around the time of the isthmian closure event. Main conclusions Our molecular phylogenetic analysis of two closely related genera of reef fishes, each with presumed trans‐isthmian geminates, cautions against the uncritical use of morphological similarity in identification of geminates, as well as the assumption that trans‐isthmian sister groups date to the isthmian closure event. These findings suggest that in some instances incomplete sampling of species within a clade including putative geminates may lead to improper conclusions regarding the pattern and timing of speciation, as well as incorrect estimation of the rate at which evolution has proceeded.