MOLECULAR PHYLOGENY OF PHYCOCYANIN‐CONTAINING CRYPTOPHYTES: EVOLUTION OF BILIPROTEINS AND GEOGRAPHICAL DISTRIBUTION1

Of 34 strains assigned to the cryptophyte genera Chroomonas Hansg., Hemiselmis Parke, and Komma D. R. A. Hill, distribution patterns of biliproteins, habitats, and sampling sites across a phylogenetic tree have been examined. The combined data set assembled from nuclear SSU rDNA, partial nuclear LSU rDNA, and nucleomorph SSU rDNA sequences comprised 4,083 positions and yielded an almost completely resolved tree. Spectrophotometry of the biliproteins and mapping of the different types of biliproteins onto the phylogenetic tree unveiled a complex evolutionary history. Different from other cryptophyte clades, the types of biliproteins were not generally congruent with clades or subclades of the genera Chroomonas (paraphyletic, phycocyanins [PCs] 645 or 630), Hemiselmis (PCs 612, 630 or phycoerythrin [PE] 555), and Komma (PC 645). At least one putative character reversal took place in the genus Chroomonas. Several changes in biliproteins have been found in the genus Hemiselmis, including two new biliprotein variants that probably originated by slight modifications from PC 612 and PE 555, respectively (PC 577 and PE 545/555). Freshwater and marine/brackish taxa were intermingled across the tree without displaying a specific pattern. In four terminal clades, genetically identical strains have been found to occur both in Europe and in the USA. The Chroomonas/Hemiselmis/Komma clade proved to be the most diverse of all cryptophyte clades concerning types of biliproteins and distribution of clades across marine or freshwater habitats.     

Species delimitation in Neotropical fishes of the genus Characidium (Teleostei,Characiformes)

Neotropical darters of the genus Characidium have a complex systematic history with several examples of sympatry throughout their distribution range in Neotropical freshwaters. Although various species within the genus have been used as models to investigate chromosomal evolution and biogeography, species boundaries and relationships still remain uncertain. Here, we use mitochondrial DNA sequences to perform species delimitation analyses within Characidium and test previous hypotheses of species richness within the Characidium zebra complex and among sympatric morphotypes of C. alipioi. Results indicate high genetic distances within tested species complexes and revealed the presence of strongly supported lineages such as the large C. lauroi group from southeastern Brazil. This suggests that the evolutionary history of these groups may be correlated with biogeographic history. Analyses also reveal that three geographically isolated populations of C. zebra represent a single species, leading us to reject prior hypothesis of multiple species. Species delimitation using mitochondrial data strongly supports the presence of two sympatric species within C. alipioi in southeastern Brazil despite limited morphological variation and conserved chromosomal patterns. These results provide a framework to further the study of systematics and evolution within Characidium.     

Evolution along the Great Rift Valley: phenotypic and genetic differentiation of East African white‐eyes (Aves,Zosteropidae)

The moist and cool cloud forests of East Africa represent a network of isolated habitats that are separated by dry and warm lowland savannah, offering an opportunity to investigate how strikingly different selective regimes affect species diversification. Here, we used the passerine genus Zosterops (white‐eyes) from this region as our model system. Species of the genus occur in contrasting distribution settings, with geographical mountain isolation driving diversification, and savannah interconnectivity preventing differentiation. We analyze (1) patterns of phenotypic and genetic differentiation in high‐ and lowland species (different distribution settings), (2) investigate the potential effects of natural selection and temporal and spatial isolation (evolutionary drivers), and (3) critically review the taxonomy of this species complex. We found strong phenotypic and genetic differentiation among and within the three focal species, both in the highland species complex and in the lowland taxa. Altitude was a stronger predictor of phenotypic patterns than the current taxonomic classification. We found longitudinal and latitudinal phenotypic gradients for all three species. Furthermore, wing length and body weight were significantly correlated with altitude and habitat type in the highland species Z. poliogaster. Genetic and phenotypic divergence showed contrasting inter‐ and intraspecific structures. We suggest that the evolution of phenotypic characters is mainly driven by natural selection due to differences in the two macro‐habitats, cloud forest and savannah. In contrast, patterns of neutral genetic variation appear to be rather driven by geographical isolation of the respective mountain massifs. Populations of the Z. poliogaster complex, as well as Z. senegalensis and Z. abyssinicus, are not monophyletic based on microsatellite data and have higher levels of intraspecific differentiation compared to the currently accepted species.     

COMPARISON OF SEED PROTEINS IN THE GENUS SUAEDA (CHENOPODIACEAE) BY MEANS OF DISC GEL ELECTROPHORESIS

Polyacrylamide gel disc electrophoresis was utilized to determine seed protein patterns in ten taxa within the genus Suaeda. The results indicated a close relationship, averaging 92.2 %, similarity between the seed protein patterns of S. maritima var. macrocarpa, S. maritima var. vulgaris, and S. maritima var. flexilis. These intraspecific forms were more similar to one another than to any of the other taxa investigated. A continental North American species, S. depressa, was related to the S. maritima complex, and its protein pattern indicates that it may have evolved from S. maritima. The technique of disc electrophoresis proved useful in assessing the degree of similarity between taxa within the genus Suaeda.     

Geographic variation and divergence of songs in the Olive Sparrow species complex

Phenotypic traits such as songs are important in species recognition. Variation in acoustic traits can form barriers to gene flow and promote speciation. Therefore, understanding song divergence is crucial in groups with controversial taxonomy such as Olive Sparrows (Arremonops rufivirgatus), a widespread Neotropical species of songbird with multiple allopatric populations. Taxonomic authorities disagree on the number of Olive Sparrow subspecies, placing them into either two or three main groups. These groups may represent separate species based on morphological traits, but trait divergence within the complex has not been examined. We studied geographic variation in the characteristics of the songs of Olive Sparrows at two geographical levels: among three proposed groups and among five allopatric populations. In a second analysis, we evaluated the strength of acoustic divergence within the complex by comparing acoustic distances among groups and allopatric populations of Olive Sparrows with the acoustic distance among three recognized species in the genus Arremonops. We analyzed 802 songs from 174 individuals across 81 locations and measured 12 variables to describe the fine structural characteristics of the songs of Olive Sparrows, Green-backed Sparrows (A. chloronotus), Black-striped Sparrows (A. conirostris), and Tocuyo Sparrows (A. tocuyensis). We found significant acoustic variation in the Olive Sparrow complex at both geographical levels. Our divergence analysis also revealed that vocal divergence within the complex is similar to or greater than that found between recognized species in the genus. Together, these results suggest that acoustic diversity within the Olive Sparrow complex probably originated by isolation in tandem with selective and/or non-selective factors.     

Phylogeography and phylogenetic relationships of Malagasy tree and ground boas

Three species of boid snakes are recognized in Madagascar, namely the genus Sanzinia (one species and two subspecies) and the genus Acrantophis (two species). In the present study, we studied the patterns of genetic variation of these species across Madagascar using a fragment of the mitochondrial 16S rRNA gene in 77 specimens. To support the phylogenetic relationships of the lineages identified, three further gene fragments (cytochrome b, 12S rRNA and c‐mos) were analyzed in a reduced but representative set of samples. The results obtained corroborate that the genus Sanzinia includes two highly divergent mitochondrial lineages that evolved independently from each other on the east versus the west side of Madagascar. Each of these lineages presents a further subdivision that separates northern from southern groups. The nuclear marker showed no variation among the Malagasy boas, indicating either very low substitution rates in this gene or relatively recent speciation events coupled with high mitochondrial substitution rates. Because the broad geographic sampling detected no admixture among haplotypic lineages within Sanzinia, it is hypothesized that these may represent distinct species. Deviant haplotypes of snakes morphologically similar to Acrantophis dumerili indicate that this taxon may be a complex of two species as well. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 640–652.     

Molecular phylogeny reveals the repeated evolution of complex male genital traits in the New Zealand moth genus Izatha (Lepidoptera: Xyloryctidae)

Male genitalia are among the most rapidly evolving and divergent morphological structures and sexual selection is known to drive this phenomenon in many taxa. Because of their diversity, even within a single genus, genital characters are frequently used to infer relationships among closely‐related species. Moths within the genus Izatha (Xyloryctidae) are ideal candidates for investigating the phylogenetic patterns of genital evolution as they display great variation in male genital structure and complexity. We determined the evolutionary relationships among 31 species of Izatha by constructing a molecular phylogeny of the genus based on the mitochondrial cytochrome oxidase subunit I gene and the isocitrate dehydrogenase and carbamoylphosphate synthase domain protein nuclear genes. This allowed estimations of ancestral male genital character states and patterns of male genital diversification using maximum‐likelihood models. The genus is divided into two well‐supported clades and two poorly supported clades at the root of the phylogeny with incomplete phylogenetic resolution within two species groups, likely due to rapid speciation. Izatha display a number of apomorphic phallic traits including cornuti (sclerotized spines) which are either discharged into the female during copulation (deciduous cornuti) or fixed to the male phallus (compound and fish‐hook cornuti). Within the genus, there is a reduction of secondary genital characters – the uncus and gnathos – but an elaboration of another grasping structure, the juxta; the potential origin and functionality of these male genital traits are discussed. Overall, some male genital characters provided a good indication of species relationships; however, several parts of the complex male genitalia of Izatha show evidence of homoplasy and convergence highlighting the problems of using these traits in determining species relationships. Additionally, this convergence has highlighted that complex genital structures may evolve repeatedly and independently within a lineage.     

Extreme variation in rates of evolution in the plastid Clp protease complex

Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multi‐subunit complexes in mitochondria and plastids. One such complex in plants is the caseinolytic protease (Clp), which plays an essential role in plastid protein turnover. The proteolytic core of Clp comprises subunits from one plastid‐encoded gene ( clpP1 ) and multiple nuclear genes. The clpP1 gene is highly conserved across most green plants, but it is by far the fastest evolving plastid‐encoded gene in some angiosperms. To better understand these extreme and mysterious patterns of divergence, we investigated the history of clpP1 molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find that clpP1 has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g. a loss of introns and RNA ‐editing sites) within seed plants. Although clpP1 is often assumed to be a pseudogene in such cases, multiple lines of evidence suggest that this is rarely true. We applied comparative native gel electrophoresis of chloroplast protein complexes followed by protein mass spectrometry in two species within the angiosperm genus Silene , which has highly elevated and heterogeneous rates of clpP1 evolution. We confirmed that clpP1 is expressed as a stable protein and forms oligomeric complexes with the nuclear‐encoded Clp subunits, even in one of the most divergent Silene species. Additionally, there is a tight correlation between amino acid substitution rates in clpP1 and the nuclear‐encoded Clp subunits across a broad sampling of angiosperms, suggesting continuing selection on interactions within this complex.     

Inflorescence patterns in the woody Brazilian genus Diplusodon (Lythraceae)

The Brazilian genus Diplusodon is the second largest genus within Lythraceae. Their 85 species occupy diverse habitats within the ‘cerrado’ vegetation, and range from shrubs and treelets to dwarf, xylopodium-bearing subshrubs. A comparative-morphological survey of their inflorescence structures using Trollian typology is here presented, as well as some evolutionary considerations drawn from mapping inflorescence characters onto a preliminary phylogeny. The inflorescences of Diplusodon are mostly polytelic, ranging from single racemes to more or less complex double-, triple-, and multiple-racemes. Frondose, compound racemes are plesiomorphic within the genus. Nevertheless, an array of derived features has been found among their species, including production of lateral cymes, proliferation of the main axis, diverse patterns of internode elongation, reduction of subtending leaves to bracts, development of accessory branches, paedomorphic flowering, and, in three species, reversion to monotely.     

Rasamsonia, a new genus comprising thermotolerant and thermophilic Talaromyces and Geosmithia species

The phylogenetic relationship among Geosmithia argillacea, Talaromyces emersonii, Talaromyces byssochlamydoides and other members of the Trichocomaceae was studied using partial RPB2 (RNA polymerase II gene, encoding the second largest protein subunit), Tsr1 (putative ribosome biogenesis protein) and Cct8 (putative chaperonin complex component TCP-1) gene sequences. The results showed that these species form a distinct clade within the Trichocomaceae and Trichocoma paradoxa is phylogenetically most closely related. Based on phenotypic and physiological characters and molecular data, we propose Rasamsonia gen. nov. to accommodate these species. This new genus is distinct from other genera of the Trichocomaceae in being thermotolerant or thermophilic and having conidiophores with distinctly rough walled stipes, olive-brown conidia and ascomata, if present, with a scanty covering. Species within the genus Rasamsonia were distinguished using a combination of phenotypic characters, extrolite patterns, ITS and partial calmodulin and β-tubulin sequences. Rasamsonia brevistipitata sp. nov. is described and five new combinations are proposed.     

Cophylogenetic analysis of lice in the Colpocephalum complex (Phthiraptera: Amblycera)

The chewing louse genus Colpocephalum parasitizes nearly a dozen distantly related orders of birds. Such a broad host distribution is relatively unusual in lice. However, the monophyly of the genus Colpocephalum has never been tested using molecular characters. Using one nuclear and one mitochondrial gene, we inferred a phylogeny for 54 lice from the genus Colpocephalum and other morphologically similar genera. The resulting phylogeny demonstrates that Colpocephalum itself is not monophyletic. However, these data support the existence of a Colpocephalum complex within which several lineages are restricted to particular host orders. These lineages corresponded to previously described genera, some of which are morphologically distinct and currently considered subgenera. Maddison–Slatkin tests were performed on the resulting phylogeny and showed that host order, host family and biogeographic region had significant phylogenetic signal when mapped onto the Colpocephalum complex phylogeny. A PARAFIT analysis comparing the overall Colpocephalum complex phylogeny to a host phylogeny revealed significant congruence between host and parasite trees. We also compared the cophylogenetic history of Colpocephalum and their hosts to that of a second distantly related feather louse genus, Degeeriella, which also infests diurnal birds of prey. Using PARAFIT to identify individual host–parasite links that contributed to overall congruence, there was no evidence of correlated cophylogenetic patterns between these two louse groups, suggesting that their host distribution patterns have been shaped by different evolutionary processes.     

Evolutionary Patterns in Pearl Oysters of the Genus <Emphasis Type="Italic">Pinctada</Emphasis> (Bivalvia: Pteriidae)

Pearl oysters belonging to the genus Pinctada (Bivalvia: Pteriidae) are widely distributed between the Indo-Pacific and western Atlantic. The existence of both widely distributed and more restricted species makes this group a suitable model to study diversification patterns and prevailing modes of speciation. Phylogenies of eight out of the 11 currently recognised Pinctada species using mitochondrial (cox1) and nuclear (18S rRNA) data yielded two monophyletic groups that correspond to shell size and presence/absence of hinge teeth. Character trace of these morphological characters onto the molecular phylogeny revealed a strong correlation. Pinctada margaritifera appears polyphyletic with specimens from Mauritius grouping in a different clade from others of the French Polynesia and Japan. Hence, P. margaritifera might represent a species complex, and specimens from Mauritius could represent a different species. Regarding the putative species complex Pinctada fucata/Pinctada martensii/Pinctada radiata/Pinctada imbricata, our molecular analyses question the taxonomic validity of the morphological characters used to discriminate P. fucata and P. martensii that exhibited the lowest genetic divergence and are most likely conspecific as they clustered together. P. radiata and P. imbricata were recovered as monophyletic. The absence of overlapping distributions between sister lineages and the observed isolation by distance suggests that allopatry is the prevailing speciation mode in Pinctada. Bayesian dating analysis indicated a Miocene origin for the genus, which is consistent with the fossil record. The northward movement of the Australian plate throughout the Miocene played an important role in the diversification process within Pinctada.     

Molecular phylogeny of the diatom genera Amphora and Halamphora (Bacillariophyta) with a focus on morphological and ecological evolution

The taxonomic history of the diatom genus Amphora is one of a broad early morphological concept resulting in the inclusion of a diversity of taxa, followed by an extended period of revision and refinement. The introduction of molecular systematics has increased the pace of revision and has largely resolved the relationships between the major lineages, indicating homoplasy in the evolution of amphoroid symmetry. Within the two largest monophyletic lineages, the genus Halamphora and the now taxonomically refined genus Amphora, the intrageneric morphological and ecological relationships have yet to be explored within a phylogenetic framework. Critical among this is whether the range of morphological features exhibited within these diverse genera are reflective of evolutionary groupings or, as with many previously studied amphoroid features, are nonhomologous when examined phylogenetically. Presented here is a four‐marker molecular phylogeny that includes 31 taxa from the genus Amphora and 77 taxa from the genus Halamphora collected from fresh, brackish, and salt waters from coastal and inland habitats of the United States and Japan. These phylogenies illustrate complex patterns in the evolution of frustule morphology and ecology within the genera and the implications of this on the taxonomy, classification, and organization of the genera are discussed.     

A molecular phylogeny of East African Amytta (Orthoptera: Tettigoniidae,Meconematinae) with data on their cytogenetics

This is the first study to address the molecular phylogeny of East African Meconematinae. We used DNA sequence data from the three genes cytochrome oxidase subunit I (COI ), 16S rRNA and histone H3 to reconstruct the relationships within the genus Amytta using Bayesian Inference and maximum likelihood. We included 45 individuals representing 19 Meconematinae taxa from Africa, Europe and Australia, and three outgroup species to explore taxonomic limits at different levels. Members of the genus Amytta belong to three related lineages within Meconematinae. Species of Amytta were found to be monophyletic with Meconema and Phlugidia as sister groups. The molecular results are in accordance with previous morphological and ecological studies. Chromosome numbers and the type of sex determination systems found in Amytta agrees with the three lineages also found in the phylogenetic tree. We conclude that the radiation of Amytta species is geological young. Biogeographical patterns caused by climatic fluctuations of the past seen also in other nonrelated Orthoptera taxa such as the coptacrine genus Parepistaurus are the drivers of biodiversity in the area.     

The immunologically conserved phycobilisome-thylakoid linker polypeptide

We have isolated phycobilisomes from two classes of red algae, several subdivisions of the cyanobacteria, and the cyanelles of Cyanophora paradoxa. In addition to the major light harvesting biliproteins, these phycobilisomes also contain several other polypeptides, the largest of which ranges from 75 to 120 kilodaltons in the different species surveyed. This protein, previously isolated and characterized from three species, was shown to be the final emitter of excitation energy in phycobilisomes and is also thought to be involved in the attachment of the phycobilisomes to the thylakoid membrane. We have obtained polyclonal antibodies to the 95 kilodalton polypeptide isolated from phycobilisomes of the cyanobacterium, Nostoc sp. This protein shares no common antigenic determinants with either the α or β subunits of allophycocyanin, or any of the other biliproteins, as determined by the sensitive Western immunoblotting technique. However, this antiserum cross-reacts with the highest molecular weight polypeptide of all the rhodophytan and cyanobacterial phycobilisomes tested. That these proteins are immunologically related, but are unrelated to other biliproteins, is reminiscent of previous immunological studies of biliproteins which showed that while the three major spectroscopically distinct classes of biliproteins (phycoerythrin, phycocyanin, and allophycocyanin) shared no common antigenic determinants, there was a strong antigenic determinant to specific biliprotein classes which crossed taxonomic divisions.     

Phylogeography of the burnet moth Zygaena transalpina complex: molecular and morphometric differentiation suggests glacial refugia in Southern France,Western France and micro‐refugia within the Alps

Patterns of common recolonization routes from glacial refugia to Central Europe during the Pleistocene are generalized to paradigms of postglacial recolonization in Europe. Recent studies indicate, however, that the actual phylogeographic history of many species might be more complex and cannot be simplified to generalized patterns. Burnet moths of the Zygaena transalpina complex represent a group of closely related taxa, which are considered as a typical example for these generalized patterns. At present, three groups are recognized that are assumed to have spread from three classical refugia in Western Europe, Italy and the Balkans to Central Europe. Here, we re‐investigate their phylogeography using a combined molecular and morphometric approach. Phylogenetic and nested clade phylogeographic analyses of 476 samples from 55 localities taken from Southern and Central Europe reveal that the Zygaena transalpina complex consists of three distinct haplotype clusters, which geographically roughly correspond to possible refugia in Western Europe, Italy and the Balkans. A synthesis of the data with a geometric morphometry dataset of 425 specimens from 46 localities corroborates this molecular result but differs in several aspects. Important new aspects are multiple refugia of the western ‘hippocrepidis’ branch and micro‐habitats within the Alps of the central ‘transalpina’ branch. Further, our results display a more complex phylogeographic pattern for this species complex, which is not tractable with a rigid, generalized pattern.     

Testing systematic concepts of Sargassum (Fucales, Phaeophyceae) using portions of the rbcLS operon

The taxonomic and phylogenetic concepts within the Sargassum C. Agardh (Sargassaceae) species complex were evaluated through molecular phylogenetic analyses using portions of the chloroplast encoded rbcLS Operon. According to more conservative sequences (rbcL), Turbinaria (Turner) J. Agardh is a close and well‐supported sister lineage to the Sargassum species complex and an appropriate external outgroup for analyses of subgenera and subsections within Sargassum. Both rbcL and more rapidly evolving rbcLS spacer sequences indicated that the East Asiatic genus Myagropsis (Mertens et Turner) Fensholt, along with Sargassum sinicola Setchell et Gardner, represent the closest lineage to Sargassum and form appropriate internal outgroups. The rbcLS spacer region supported three of four subgeneric designations by J. Agardh and sectional levels within the subgenus Sargassum. However, some aspects of Agardh's system were not supported: many of the subsectional ranks or the phyletic concepts; Phyllotrichia was not monophyletic as a subgenus, and its species were also not the most ancestral of Sargassum; and subgenus Sargassum was not the most derived subgenus within the genus. This modern phylogeny suggests a deep evolutionary history for subgenus Sargassum with rapid speciation in closely related subsections and series, and a sister relationship between subgenera Arthrophycus and Bactrophycus.     

凝胶电泳与共头霉分类

对于共头霉的唯一已知种总状共头霉Syncephalastrum racemosum Cohn ex Schroet.(S 1)和新发现的具单孢孢子囊的新种单孢共头霉下的三个变种,原变种S.monosporum Zheng et al. var. monosporum( S7, S8, S9),冠囊变种var. cristatum Zheng et al. (S10, S11)及多重生变种var. pluriproliferum Zheng et al.(S12) 6株菌的蛋白和酯酶进行了聚丙烯酰胺凝胶电泳的研究.这4个分类群的蛋白图谱和酯酶酶谱互不相同,而同一分类群内各个菌株之间则有很高的相似性.从计算出的相似性百分数来看,3个新变种相互之间有较为密切的关系,而和S. racemosum虽然较疏远,但也有相当程度的亲缘关系.这些结果被认为支持了根据形态鉴定而定这三个新变种属于同一新种内并将其和S. racemosum一并归属于一个属内.由此可见,聚丙烯酰胺凝胶电泳是共头霉分类的有用的辅助手段.     

The geometry of gender: hyper‐diversification of sexual systems in Urtica L. (Urticaceae)

Urtica L. (Urticaceae) is generally reported as a genus of monoecious and dioecious taxa. However, the gender information found in the literature does not at all reflect the actual diversity of gender patterns in Urtica. Dioecy appears to be truly absent from Urtica, but otherwise there has been a major diversification in the geometry of gender and no comparable patterns exist in other plant groups. Thus, we here define technical terms for all unique architectural types of monoecy found in Urtica and closely related genera and reconstruct the ancestral gender states in a Bayesian framework. Our studies are based on a near‐comprehensive sampling, including 61 of the 63 Urtica species recognized. We report polygamy, two types of gynodioecy and five different architectural types of monoecy. A total of 15 switches appear to have taken place within the genus. Although gender characteristics have diversified strongly, they are relatively conserved within clades. Monoecy is the predominant sexual system within Urtica and specifically basiandrous monoecy (i.e. basal inflorescence branches of each individual male only, apical branches female) is the most widespread type, reported for 11 different clades. In particular, it characterizes the basally branching pilulifera‐clade and the sister genus Zhengyia, and may thus represent the plesiomorphic condition for Urtica. Gender distribution and gross morphology appear to evolve largely independently from each other and gender distribution is largely independent of growth habit. However, polygamous taxa are most common amongst rhizomatous perennials (one‐third of the taxa).     

Comparative phylogeography of mainland and insular species of Neotropical molossid bats (Molossus)

Historical events, habitat preferences, and geographic barriers might result in distinct genetic patterns in insular versus mainland populations. Comparison between these two biogeographic systems provides an opportunity to investigate the relative role of isolation in phylogeographic patterns and to elucidate the importance of evolution and demographic history in population structure. Herein, we use a genotype‐by‐sequencing approach (GBS) to explore population structure within three species of mastiff bats (Molossus molossus, M. coibensis, and M. milleri), which represent different ecological histories and geographical distributions in the genus. We tested the hypotheses that oceanic straits serve as barriers to dispersal in Caribbean bats and that isolated island populations are more likely to experience genetic drift and bottlenecks in comparison with highly connected ones, thus leading to different phylogeographic patterns. We show that population structures vary according to general habitat preferences, levels of population isolation, and historical fluctuations in climate. In our dataset, mainland geographic barriers played only a small role in isolation of lineages. However, oceanic straits posed a partial barrier to the dispersal for some populations within some species (M. milleri), but do not seem to disrupt gene flow in others (M. molossus). Lineages on distant islands undergo genetic bottlenecks more frequently than island lineages closer to the mainland, which have a greater exchange of haplotypes.