Biogeography of ‘Cyprinella lutrensis’: intensive genetic sampling from the Pecos River ‘melting pot’ reveals a dynamic history and phylogenetic complexity

Thorough sampling is necessary to delineate lineage diversity for polytypic ‘species’ such as Cyprinella lutrensis. We conducted extensive mtDNA sampling (cytochrome b and ND4) from the Pecos River, Rio Grande, and South Canadian River, New Mexico. Our study focussed on the Pecos River due to its complex geological history and potential to harbour multiple lineages. We used geometric–morphometric, morphometric, and meristic analyses to test for phenotypic divergence and combined nucDNA with mtDNA to test for cytonuclear disequilibrium and combined our sequences with published data to conduct a phylogenetic re‐assessment of the entire C. lutrensis clade. We detected five co‐occurring mtDNA lineages in the Pecos River, but no evidence for cytonuclear disequilibrium or phenotypic divergence. Recognized species were interspersed amongst divergent lineages of ‘C. lutrensis’. Allopatric divergence among drainages isolated in the Late Miocene and Pliocene apparently produced several recognized species and major divisions within ‘C. lutrensis’. Pleistocene re‐expansion and subsequent re‐fragmentation of a centralized lineage founded younger, divergent lineages throughout the Rio Grande basin and Edwards Plateau. There is also evidence of recent introductions to the Rio Grande, Pecos and South Canadian Rivers. Nonetheless, deeply divergent lineages have coexisted since the Pleistocene.     

Sympatric speciation in a genus of marine reef fishes

Sympatric speciation has been contentious since its inception, yet is increasingly recognized as important based on accumulating theoretical and empirical support. Here, we present a compelling case of sympatric speciation in a taxon of marine reef fishes using a comparative and mechanistic approach. Hexagrammos otakii and H. agrammus occur in sympatry throughout their ranges. Molecular sequence data from six loci, with complete sampling of the genus, support monophyly of these sister species. Although hybridization occurrs frequently with an allopatric congener in an area of slight distributional overlap, we found no F₁ hybrids between the focal sympatric taxa throughout their coextensive ranges. We present genetic evidence for complete reproductive isolation based on SNP analysis of 382 individuals indicating fixed polymorphisms, with no shared haplotypes or genotypes, between sympatric species. To address questions of speciation, we take a mechanistic approach and directly compare aspects of reproductive isolation between allopatric and sympatric taxa both in nature and in the laboratory. We conclude that the buildup of reproductive isolation is strikingly different in sympatric vs. allopatric taxa, consistent with theoretical predictions. Lab reared hybrids from allopatric species crosses exhibit severe fitness effects in the F₁ or backcross generation. No intrinsic fitness effects are observed in F₁ hybrids from sympatric species pairs, however these treatments exhibited reduced fertilization success and complete pre‐mating isolation is implied in nature because F₁ hybrid adults do not occur. Our study addresses limitations of previous studies and supports new criteria for inferring sympatric speciation.     

The Biogeography of Tropical Phytoplankton Species in the Pacific Ocean

The ranges of 10 tropical Pacific phytoplankton species are shown in the maps. Five types of these ranges are discussed. Except for broadly tropical species some species with much narrower ranges are characterized. The bases of ranges and the expatriation areas are given. The bases of ranges of all the species studied fall into similar temperature and salinity limits. Most of the species inhabit a wide range of nutrients concentration, but Climacodium frauenfeldianum and Hemiaulus hauckii are only found at low phosphate and silicate concentrations. These peculiarities determine the geography of ranges of these two species. Among the species investigated only Ceratium gravidum belongs to the shade flora.     

Phylogeography of the flag cabrilla Epinephelus labriformis (Serranidae): implications for the biogeography of the Tropical Eastern Pacific and the early stages of speciation in a marine shore fish

Aim To examine the role of previously described biogeographical boundaries in shaping phylogeographical relationships within and among two putative eastern Pacific sibling species, the flag cabrilla, Epinephelus labriformis and the Clipperton grouper, Epinephelus clippertonensis (Serranidae). Location Tropical Eastern Pacific (TEP). Methods Sequence data from the mitochondrial cytochrome b gene were obtained from samples throughout the range of the species. Coalescence analysis, mismatch distributions and an analysis of molecular variance (amova ) were used to infer population differentiation. Results Overall, 49 haplotypes were found among 304 specimens, and there was significant structure corresponding to geographical locality (amova , Φ_ct = 0.198, P < 0.001; Φ_st = 0.207, P < 0.001; F_st = 0.169, P < 0.001; F_ct = 0.151, P = 0.036). Coalescence analysis indicates a population expansion at Clipperton Atoll during the mid‐Pleistocene. Main conclusions Our results suggest that previously described barriers to dispersal along the mainland of the TEP may not impinge on the dispersal ability of marine species, such as these groupers, that have long‐lived pelagic larvae. In contrast, gene flow between mainland and island populations of the readily distinguishable morphospecies E. labriformis and E. clippertonensis is restricted. The low level of genetic differentiation between the two species indicates that changes in external colour patterns may evolve more rapidly than genetic markers commonly used to delimit species boundaries. Thus a combination of colour differences and a lack of reciprocal monophyly may act as good indicators of incipient speciation in the marine environment.     

Allopatry and overlap in a clade of snails from mangroves and mud flats in the Indo‐West Pacific and Mediterranean (Gastropoda: Potamididae: Cerithideopsilla)

Cerithideopsilla is a genus of potamidid snails found in high abundance on sedimentary intertidal flats and beneath mangrove trees on continental shores in the tropical and subtropical Indo‐West Pacific region and Mediterranean Sea. Taxonomic revisions have recognized four species, but recent molecular studies have hinted at a higher diversity. Here, we analyse 377 individuals sampled from across the known range and use a combination of molecular phylogenetic (mitochondrial COI and 16S rRNA, and nuclear 28S rRNA genes), statistical (generalized mixed Yule‐coalescent GMYC method) and morphological (shell form) criteria to delimit 16 species. These form four species groups, corresponding with the traditionally recognized species C. alata, C. ‘djadjariensis’ (for which the valid name is C. incisa), C. cingulata and C. conica. Distribution maps were compiled using museum specimens identified by diagnostic shell characters. In combination with the molecular phylogenetic trees, these suggest an allopatric speciation mode, with diversification centred on the East Asian coastline and northern Australia, and a pronounced gap in the ‘eastern Indonesian corridor’, an area of low oceanic productivity. There is, however, frequently geographical overlap between sister species and we suggest from several sources of evidence (e.g. presence of C. conica in isolated saline lakes 900 km from the sea) that post‐speciation transport by migratory birds has occurred. Nine of the 16 species occur between the Gulf of Tonkin and Hong Kong, so southern China is significant for both the evolution and conservation of Cerithideopsilla species. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 114 , 212–228.     

Phylogenetic Cascades and the Origins of Tropical Diversity

For organisms involved in specialized ecological interactions, the potential exists to have congruent evolutionary histories, such that diversification within one lineage of organisms parallels diversification within another. This model of shared evolutionary history has most often been explored in a bitrophic context, particularly with plants and specialized herbivorous insects, though also with other ecological partners such as vertebrate hosts and their invertebrate parasites. Recently, the possibility has been raised that evolutionary histories might be shared across more than two trophic levels, a phenomenon that we term a phylogenetic cascade. We review previous work on tritrophic diversification and discuss outstanding questions, with an emphasis on plants, caterpillars, and parasitoids, in diverse tropical communities.     

Distribution,host plant affiliation,phenology, and phylogeny of walnut‐infesting Rhagoletis flies (Diptera: Tephritidae) in Mexico

Many taxa of Nearctic origin have diversified in the subtropical highlands of Mexico. In particular, flies in the genus Rhagoletis have undergone episodes of isolation and gene flow during Pleistocene glaciations and post‐glacial times that have produced lineage differentiation and reproductive isolation. To reach a better understanding of the phylogeography of the genus Rhagoletis, a host plant survey of the walnut‐infesting Rhagoletis suavis species group was conducted across sixteen states comprising 34 different collecting sites in Mexico over a 9‐year period. Five species of Juglans were found to be infested by three species of walnut‐attacking Rhagoletis flies. Several species of parasitoids were also recovered from collections, but in contrast to their walnut fly hosts, they revealed little evidence for host or geographic subdivision. There was no consistent difference in mean eclosion time between walnut fly species or populations associated with different host walnuts in Mexico, unlike the case for other Rhagoletis species, in which allochronic isolation arising from variation in diapause timing is a major ecological adaptation, reproductively isolating flies. We compare the distribution of R. suavis flies in Mexico with those of other Rhagoletis species attacking hawthorns and cherries, and discuss its implications for population divergence and speciation. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 765–779.     

Vertical distribution and phylogenetic composition of bacteria in the Eastern Tropical North Pacific Ocean

The vertical community structure of bacteria along a depth profile in the Eastern Tropical North Pacific Ocean (13 degrees N, 104 degrees W) was studied by flow cytometry measurement and 16S rRNA gene clone libraries analysis. Picoeukaryotes and Synechococcus peaked at 30 m and decreased sharply below 50 m, while Prochlorococcus peaked at both 30 and 100 m layers and disappeared below 200 m. Heterotrophic bacteria peaked above shallow thermocline and decreased along the depth profile. Sequences of total 322 clones from four clone libraries (10, 100, 1000, and 3000 m) clustered into nine major lineages. gamma-Proteobacteria dominated all the depths and occupied almost the whole bacterial community at the 3000 m. alpha-Proteobacteria was abundant throughout the water column except near the sea bottom, and delta-Proteobacteria peaked at the 1000 m depth. Cyanobacteria were primarily limited to the photic zone, and the genetic diversity of Prochlorococcus showed a good correlation with niche adaptation. The appearance of the Cytophaga-Flexibacter-Bacteroides (CFB) group did not show a clear relationship with depth. Actinobacteria were found both in the photic zone and in deep water. Planctomyetes, Acidobacteria, and Verrucomicrobia were present as minor groups and more dominant in the deeper layers of water.     

Disentangling the genetic and morphological structure of Patella candei complex in Macaronesia (NE Atlantic)

The uptake of natural living resources for human consumption has triggered serious changes in the balance of ecosystems. In the archipelagos of Macaronesia (NE Atlantic), limpets have been extensively exploited probably since islands were first colonized. This has led to profound consequences in the dynamics of rocky shore communities. The Patella candei complex includes various subspecies of limpets that are ascribed to a particular archipelago and has been the focus of several taxonomic surveys without much agreement. Under a conservational perspective, we apply morphometric and genetic analyses to test subspecies boundaries in P. candei and to evaluate its current population connectivity throughout Macaronesia (Azores, Madeira, and Canaries). A highly significant genetic break between archipelagos following isolation by distance was detected (F_ST = 0.369, p < .001). Contrastingly, significant genetic differentiation among islands (i.e., Azores) was absent possibly indicating ongoing gene flow via larval exchange between populations. Significant shell‐shape differences among archipelagos were also detected using both distance‐based and geometric morphometric analyses. Adaptive processes associated with niche differentiation and strong barriers to gene flow among archipelagos may be the mechanisms underlying P. candei diversification in Macaronesia. Under the very probable assumption that populations of P. candei from each archipelago are geographically and/or ecologically isolated populations, the various subspecies within the P. candei complex may be best thought of as true species using the denomination: P. candei in Selvagens, Patella gomesii in Azores, Patella ordinaria in Madeira, and Patella crenata for Canaries. This would be in agreement with stock delimitation and units of conservation of P. candei sensu latu along Macaronesia.     

Biogeography of mammals on tropical Pacific islands

Aim We examine the influence of geography on species richness and endemism of mammals on tropical Pacific archipelagos to determine the importance of intra‐ and inter‐archipelago speciation in promoting local and regional species richness. Location Thirty tropical Pacific archipelagos. Methods A distributional list of mammals on 30 archipelagos was compiled, and values for 10 geographical variables were estimated for each archipelago. Mammal species were placed in three different categories (continental, Pacific and endemic) based on their distribution. The total number of species and numbers of species within each category were related to the geographical variables using Poisson regression analysis. Results Species richness was related positively to variables describing land area, numbers of large islands and elevation; and negatively to variables describing isolation. Levels of endemism did not differ between volant and non‐volant species, but differed between mega‐ and microchiropterans. Main conclusions Variation in species richness of mammals in the tropical Pacific region can be accounted for by a combination of intra‐archipelago speciation within archipelagos composed of large islands, and inter‐archipelago speciation, particularly among more isolated archipelagos. Mammals were less widely distributed throughout the study area than previously found for butterflies, skinks or birds. However, the level of endemism was similar to that of skinks and birds on the same archipelagos, and was higher than that of butterflies.     

Factors shaping the range-size frequency distribution of the endemic fish fauna of the Tropical Eastern Pacific

Aim To assess the effect of habitat fragmentation and isolation in determining the range‐size frequency distribution (RFD) of the shorefish fauna endemic to a discrete biogeographical region. Location The Tropical Eastern Pacific (TEP). Methods Habitat isolation represents the separation between oceanic islands and the continental shore of the TEP and habitat fragmentation the degree of spatial continuity of habitats (i.e. reefs, soft bottom, nearshore waters) along the continental coast of the TEP. The effects of habitat isolation and fragmentation were quantified by comparing the RFDs of (1) the species found on oceanic islands vs. the continental shore, and (2) species on the continental shore that use different habitat types. Results The RFD of the entire TEP fauna was bimodal, with peaks at both small‐ and large‐range ends of the spectrum. The small‐range peak was due almost entirely to island species and the large‐range peak due mainly to species found in both the continental shore and oceanic islands. RFDs varied among species using different habitats on the continental shore: reef‐fishes had a right‐skewed RFD, soft‐bottom species a flat RFD, and coastal‐pelagic fishes a left‐skewed RFD. Main conclusions Variation in dispersal capabilities associated with habitat isolation and fragmentation in the TEP appears to be the main mechanism contributing to differences among RFD structure, although variation in tolerances arising from the dynamic regional environment may contribute to some patterns. Because diversity patterns are strongly affected by RFD structure, it is now evident that the insular and continental components of a fauna should be treated separately when analysing such patterns. Furthermore, contrasts in RFD structure among species using different habitats demonstrate that a full understanding of the causes of diversity patterns requires analyses of complete regional faunas in relation to regional geography.     

Phylogeographic history of the genus Tropheus,a lineage of rock-dwelling cichlid fishes endemic to Lake Tanganyika

Lake Tanganyika contains the oldest and most complex flock of cichlid fishes counting about 200 endemic species. It is comprised of 16 ecologically, morphologically and genetically highly distinct tribes. Many species are further subdivided into arrays of geographic morphs, each colonizing particular sections of the shore line. The genus Tropheus represents the most spectacular and best studied example for this phenomenon, counting more than 100 distinctly colored populations and sister species, some living in sympatry. Their present distribution and genetic structure was shaped by a series of lake level fluctuations which caused cycles of isolation and secondary admixis. The present study extends previous work on the phylogeography of Tropheus and aims at the fine-scale reconstruction of the origin and spread of lineages in the central and southern basin of the lake. The previously defined mtDNA lineages were evaluated on the basis of statistical parsimony networks. Haplotype networks were created for each lineage and related to their centers of diversity in terms of present distribution. A linearized tree analysis and a mismatch distribution analysis corroborate two of the three radiation waves suggested in earlier works, but the new data suggest a different primary colonization scenario for the southern basin.     

Bacterioplankton nutrient metabolism in the Eastern Tropical North Pacific

Bacterioplankton nutrient metabolism in the Eastern Tropical North Pacific (ETNP) was assessed using specific activities of intracellular nitrogen (N) assimilation enzymes and hydrolytic ectoenzymes during amendment experiments, mesocosms, and diel studies of in situ rates. Glutamine synthetase (GS) and assimilatory nitrate reductase (ANR) were used to investigate N bioavailability, alkaline phosphatase (AP) to assess phosphorous (P) bioavailability and β-glucosidase (β-Glu) to detect shifts in the use of labile dissolved organic carbon (DOC). Conditions regulating activity of each enzyme were tested using incubations of < 0.6 mm size-fractionated seawater amended with different combinations of N, P, and DOC as glucose. Overall, N-deficiency was indicated by pronounced growth stimulation and repression of GS and ANR activity in incubations amended with dissolved free amino acid and ammonium. Phosphate and glucose amendments produced little or no growth stimulation, but did influence activity of all enzymes measured. Enzyme activities of bacterioplankton in mesocosms of whole plankton indicated enhanced N-deficiency and glucoside hydrolysis when the plankton community was released from any P-deficiency. Spatially, enzyme activity of bacterioplankton during two diel studies (at one slope and one open-ocean station) suggested greater N-deficiency at surface depths than within the chlorophyll maximum where activity of AP and b-Glu was often greatest. There was also greater GS and ANR activity at the open-ocean station, which had lower concentrations of dissolved inorganic N (DIN) relative to soluble reactive P (SRP), than along the continental slope of Mexico. These data suggest that bacterioplankton in surface waters of the ETNP require a large flux of DOC to drive N-deficiency; whereas, bacterioplankton deeper in the chlorophyll maximum depend on hydrolysis of complex DOC and DOP to meet their carbon demand in the presence of elevated nutrients with a low DIN:SRP ratio.     

Biogeography of lemurs in the humid forests of Madagascar: the role of elevational distribution and rivers

Aim Elucidation of the influence of river systems on the distribution of lemurs. Location Humid forests of Madagascar. Methods We review the elevational distribution of Malagasy lemurs to address hypotheses of the role of rivers as physical barriers. Main conclusions Rivers are barriers for some species. However, several lemurs have altitudinal ranges that are higher than the headwaters of a given river, and in such cases these species are able to disperse across the source.     

Rejecting strictly allopatric speciation on a continental island: prolonged postdivergence gene flow between Taiwan (Leucodioptron taewanus,Passeriformes Timaliidae) and Chinese (L. canorum canorum) hwameis

Allopatry is conventionally considered the geographical mode of speciation for continental island organisms. However, strictly allopatric speciation models that assume the lack of postdivergence gene flow seem oversimplified given the recurrence of land bridges during glacial periods since the late Pliocene. Here, to evaluate whether a continental island endemic, the Taiwan hwamei (Leucodioptron taewanus, Passeriformes Timaliidae) speciated in strict allopatry, we used weighted‐regression‐based approximate Bayesian computation (ABC) to analyse the genetic polymorphism of 18 neutral nuclear loci (total length: 8500 bp) in Taiwan hwamei and its continental sister species, the Chinese hwamei (L. canorum canorum). The nonallopatry model was found to fit better with observed genetic polymorphism of the two hwamei species (posterior possibility = 0.82). We also recovered unambiguous signals of nontrivial bidirectional postdivergence gene flow (N_em » 1) between Chinese hwamei and Taiwan hwamei until 0.5 Ma. Divergence time was estimated to be 3.5 to 2 million years earlier than that estimated from mitochondrial cytochrome b sequences. Finally, using the inferred nonallopatry model to simulate genetic variation at 24 nuclear genes examined showed that the adiponectin receptor 1 gene may be under divergent adaptation. Our findings imply that the role of geographical barrier may be less prominent for the speciation of continental island endemics, and suggest a shift in speciation studies from simply correlating geographical barrier and genetic divergence to examining factors that facilitate and maintain divergence, e.g. differential selection and sexual selection, especially in the face of interpopulation gene flow.     

Nest-site size as a short-term constraint on the reproductive success of paternal fishes

Synopsis Because female signal blennies, Emblemaria hypacanthus (Pisces: Chaenopsidae), exhibited a preference for the larger of two males in laboratory mate-choice experiments, male reproductive success was predicted to be positively correlated with male size in field populations. This prediction was met at one field site, but not a second where shelter size, rather than male size, was the primary correlate of male reproductive success. This finding appeared to be the consequence of the relatively small size of shelters (vacant gastropod shells) at the second site. At this site, significantly more males had their shelters filled with eggs and variance in male reproductive success was lower than at the first site. Limited area for deposition of eggs is potentially an important constraint on the short-term reproductive success of paternal males of shelter- or crevice-spawning fishes.