SPECIES FLOCK IN THE NORTH AMERICAN GREAT LAKES: MOLECULAR ECOLOGY OF LAKE NIPIGON CISCOES (TELEOSTEI: COREGONIDAE: COREGONUS)

Studies on north temperate fish species indicate that new habitat availability following the last ice sheet retreat has promoted ecological speciation in postglacial lakes. Extensive ecophenotypic polymorphisms observed among the North American Great Lakes ciscoes suggest that this fish group has radiated through trophic adaptation and reproductive isolation. This study aims at relating the ecomorphological and genetic polymorphisms expressed by the Lake Nipigon ciscoes to evaluate the likelihood of an intralacustrine divergence driven by the exploitation of alternative resources. Morphological variation and trophic and spatial niches are characterized and contrasted among 203 individuals. Genetic variation at six microsatellite loci is also analyzed to appraise the extent of genetic differentiation among these morphotypes. Ecomorphological data confirm the existence of four distinct morphotypes displaying various levels of trophic and depth niche overlap and specialization. However, ecological and morphological variations were not coupled as expected, suggesting that trophic morphology is not always predictive of ecology. Although extensive genetic variability was observed, little genetic differentiation was found among morphotypes, with only one morph being slightly but significantly differentiated. Contrasting patterns of morphological, ecological, and genetic polymorphisms did not support the hypothesis of ecological speciation: the most ecologically different forms were morphologically most similar, while the only genetically differentiated morph was the least ecologically specialized. The low levels of genetic differentiation and the congruence between θ and φ estimates altogether suggest a recent (most likely postglacial) process of divergence and/or high gene flow among morphs A, C, and D, whereas higher φ estimates for comparison involving morph B suggest that this morph may be derived from another colonizing lineage exchanging little genes with the other morphs. Patterns of ecophenotypic and genetic diversity are also compatible with a more complex evolutionary history involving hybridization and introgression.     

Phenotypic variability in the Caribbean Orange Icing sponge Mycale laevis (Demospongiae: Poecilosclerida)

Sponge species may present several morphotypes, but sponges that are morphologically similar can be separate species. We investigated morphological variation in Mycale laevis, a common Caribbean reef sponge. Four morphotypes of M. laevis have been observed (1) orange, semi-cryptic, (2) orange, massive, (3) white, semi-cryptic, and (4) white, massive. Samples of M. laevis were collected from Key Largo, Florida, the Bahamas Islands, and Bocas del Toro, Panama. Fragments of the 18S and 28S rRNA ribosomal genes were sequenced and subjected to phylogentic analyses together with sequences obtained for 11 other Mycale species and additional sequences retrieved from GenBank. Phylogenetic analyses confirmed that the genus Mycale is monophyletic within the Order Poecilosclerida, although the subgenus Aegogropila is polyphyletic and the subgenus Mycale is paraphyletic. All 4 morphotypes formed a monophyletic group within Mycale, and no genetic differences were observed among them. Spicule lengths did not differ among the 4 morphotypes, but the dominant megasclere in samples collected from Florida and the Bahamas was the strongyle, while those from Panama had subtylostyles. Our data suggest that the 4 morphotypes constitute a single species, but further studies would be necessary to determine whether skeletal variability is due to phentotypic or genotypic plasticity.     

Polymorphism in a common Atlantic reef coral (Montastraea cavernosa) and its long-term evolutionary implications

Recent advances in morphometrics and genetics have led to the discovery of numerous cryptic species in coral reef ecosystems. A prime example is the Montastraea annularis scleractinian coral species complex, in which morphological, genetic, and reproductive data concur on species boundaries, allowing evaluation of long-term patterns of speciation and evolutionary innovation. Here we test for cryptic species in the Atlantic species, Montastraea cavernosa, long recognized as polymorphic. Our modern samples consist of 94 colonies collected at four locations (Belize, Panamá, Puerto Rico in the Caribbean; S?o Tomé in the Eastern Atlantic). Our fossil samples consist of 78 colonies from the Plio-Pleistocene of Costa Rica and Panamá. Landmark morphometric data were collected on thin sections of 46 modern and 78 fossil colonies. Mahalanobis distances between colonies were calculated using Bookstein coordinates, revealing two modern and four fossil morphotypes. The remaining 48 of the 94 modern colonies were assigned to morphotype using discriminant analysis of calical measurements. Cross-tabulation and multiple comparisons tests show no significant morphological differences among geographic locations or water depths. Patterns of variation within and among fossil morphotypes are similar to modern morphotypes. DNA sequence data were collected for two polymorphic nuclear loci (β-tub1 and β-tub2) on all 94 modern colonies. Haplotype networks show that both genes consist of two clades, but morphotypes are not associated with genetic clades. Genotype frequencies and two-locus genotype assignments indicate genetic exchange across clades, and ϕst values show no genetic differentiation between morphotypes at different locations. Taken together, our morphological and genetic results do not provide evidence for cryptic species in M. cavernosa, but indicate instead that this species has an unusually high degree of polymorphism over a wide geographic area and persisting for >25 million years (myr).     

Conservation genetics of whales and dolphins

Whales and dolphins (cetaceans) are found in all the world's oceans and in some of the major rivers, yet little is known about the distribution and behaviour of many species. At the same time, cetaceans are under threat from a variety of pressures including direct and indirect takes, pollution, and competition for habitat and prey. To ensure their long-term survival it will be necessary to preserve genetic diversity through the identification and protection of differentiated populations, the assessment of variation within local populations, and through a better understanding of reproductive and dispersal behaviour. The application of molecular genetic techniques is helping to provide answers to some of these previously intractable questions. Early results suggest few consistent patterns. Obvious geographic boundaries correlate to genetic distance in some species, and not in others. Furthermore, morphological variation within species can be fairly extensive without correlating to genetic distance, or relatively minor between morphotypes that are as genetically distinct as some species. These examples emphasize the need for further study.     

Population structure, history and gene flow in a group of closely related land snails: genetic variation in Partula from the Society Islands of the Pacific

Previous studies of Partula land snails from the Society Islands, French Polynesia, have shown that populations within species are highly differentiated in terms of their morphology, behaviour, ecology and molecular genetic variation. Despite this level of variability, differences between species are sometimes small, possibly reflecting the fact that reproductive isolation is not always complete and there exists the opportunity for genetic exchange between taxa through hybridization. The present study uses sequence data from a mitochondrial gene to further investigate genetic variation in Society Island Partula. Most populations are found in this study to be highly differentiated, but within individual species there seems to be no simple relationship either between genetic distance and geographical proximity, or between variation in mitochondria and that in allozymes or morphological characteristics. Among species there appears to be no simple correlation between degrees of reproductive isolation and genetic relatedness according to mitochondrial DNA. The results suggest that past events as well as ongoing drift and selection may have been important in affecting patterns of variation. Similarities among species at specific localities suggest that there must have been some genetic exchange in the past, although this may not necessarily reflect ongoing rates of hybridization. The discrepancy between results for different markers probably reflects the differential effects of drift and selection on mitochondrial and nuclear genes.     

The genomics of speciation: investigating the molecular correlates of X chromosome introgression across the hybrid zone between Mus domesticus and Mus musculus

Understanding the genetic details of reproductive isolation is a key goal in the study of speciation. Hybrid zones, geographical regions where two species meet and exchange genes, can provide insight into the genetic basis of reproductive isolation. This is especially true in species with mapped molecular markers because patterns of gene flow can be compared among different genomic regions. Even greater insight can be obtained in species with complete genome sequences because gene identity, gene number and other features of interest can be assessed for genomic regions with different patterns of introgression. Here, we review recent studies on the well-characterized hybrid zone between Mus domesticus and M. musculus , including a detailed survey of patterns of introgression for 13 markers on the X chromosome. We then compare levels of introgression for these 13 regions to a number of genomic attributes inferred from the complete sequence of the X chromosome, with two purposes. First, we identify candidate genes for reproductive isolation by finding genes that map to an X-linked region of reduced introgression and that are only expressed in the male germ line or that show high rates of protein evolution in comparison with rat. Second, we ask whether patterns of gene flow are correlated with recombination rate, gene density, base composition, CpG island density, mutation rate and the rate of protein evolution, as might be expected if many genes contribute to reproductive isolation. We identify seven candidate genes for reproductive isolation between M. domesticus and M. musculus , and our analyses reveal no general correlations between levels of introgression and other measured sequence characteristics. These results underline the utility of the house mouse as a model system for the study of speciation.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 523–534.     

Even more oak species in Mexico? Genetic structure and morphological differentiation support the presence of at least two specific entities within Quercus laeta

Differentiation among populations, sometimes despite ongoing gene exchange, is a key step in speciation. Therefore, comparison of intra- and interspecific differentiation patterns is of great significance to understanding speciation. The genus Quercus is an interesting system to test speciation models in the presence of gene flow, due to its weak interspecific reproductive barriers. The aim of the present study was to characterize the degree and pattern of morphological and genetic differentiation among different morphotypes in the white oak Quercus laeta, some corresponding to the previously described species Quercus centralis, Q. laeta, Quercus prinopsis, and Quercus transmontana, as well as geographically structured variation within Q. transmontana not described previously. Our goal was to evaluate if some of these can be considered distinct specific entities or are rather part of a continuum of variation. Nine microsatellite loci and two intergenic regions of chloroplast DNA were analyzed. Morphological differences were evaluated using geometric morphometrics. Chloroplast DNA showed low differentiation, suggesting introgression or sharing of ancestral haplotypes among the Q. laeta morphotypes. Nuclear microsatellites indicated differentiation into two distinct main genetic groups, which were congruent with morphological differentiation. In conclusion, nuclear markers and morphological variations suggest the existence of at least two different entities within Q. laeta.     

Sexual hybridization experiments and phylogenetic relationships as inferred from rubisco spacer sequences in the genus alaria (phaeophyceae)

Alaria (Alariaceae, Phaeophyceae) is a common genus of kelps generally found in the lower intertidal and shallow subtidal regions of rocky shores subject to strong wave exposure. Fourteen species are currently recognized, of which 11 are found in the cold–temperate North Pacific Ocean. Alaria esculenta (L.) Greville, the type species described from the North Atlantic, exhibits a range of biogeographically correlated morphotypes indicating the possibility of multiple species, subspecies, and/or hybrids. This has led to an unstable taxonomy. We compared five species from the Atlantic and Pacific, including six North Atlantic isolates of A. esculenta. Phylogenetic analyses based on Rubisco spacer sequences resulted in a well-resolved topology of these five species, but did not distinguish between the six biogeographic isolates of A. esculenta. Laboratory hybridization experiments among four A. esculenta isolates showed partial intrafertility. Among five tested Alaria species, interfertility as well as fertility barriers were encountered, inconsistent with reproductive isolation. The data reject both a biological and morphological species concept and support only a phylogenetic species concept for Alaria , demonstrating that morphological variation has evolved independently of molecular variation in the genes under investigation in the species of the genus Alaria.     

Genetic differences among three colour morphotypes of the black rockfish,Sebastes inermis,inferred from mtDNA and AFLP analyses

The genetic differences among three colour morphotypes of the black rockish, Sebastes inermis, were determined from mitochondrial DNA (mtDNA) and amplified fragment length polymorphisms (AFLP) analyses. In the AFLP analysis, each morphotype could be distinguished by the presence or absence matrix of five AFLP loci. These diagnostic loci indicated that the three morphotypes represented independent gene pools, indicating reproductive isolation. Furthermore, 14 significant frequency differences in AFLP fragments were observed between morphotypes A and B, 12 between morphotypes A and C and six between morphotypes B and C. These significant differences also supported the likelihood of reproductive isolation among the morphotypes. In the mtDNA analysis, variations in partial sequences of the control region failed to distinguish clearly between the three morphotypes, but restrictions of gene flow and genetic differentiation among the morphotypes were supported by significant FST estimates. The absence of diagnostic mtDNA differences in this study may have been due to introgressive hybridization among the morphotypes and/or incomplete lineage sorting, due to the recency of speciation.     

Patterns of intraspecific diversification in the Piriqueta caroliniana complex in southeastern North America and the Bahamas

Abstract.— We use chloroplast DNA (cpDNA) variation and nested clade phylogeographic analyses to infer the historical processes that have contributed to the high level of morphological and ecological diversification present in a group of herbaceous perennials (the Piriqueta caroliniana complex) in North America and the Bahamas. The presence of morphologically distinct and intercompatible varieties (morphotypes) that can be distinguished based on suites of taxonomic characters (e.g., leaf shape, pubescence type, stature) and contrasting habitat affinities (from marshes to dry pinelands and sand scrub) makes this group particularly appropriate for studies of intraspecific diversification. To examine the distribution of haplotypes among populations, we sampled 467 individuals from 55 locations in Florida, Georgia, and the northern Bahamas (Grand Bahama and Abaco) and screened each individual for cpDNA variation using restriction fragment length polymorphism (RFLP) and heteroduplex analyses. We develop a one-step haplotype phylogeny for this group and use the geographic distributions of haplotypes and clades to test specific phylogeographic hypotheses using the methods developed by Templeton and his colleagues (Templeton 1998). In general, the distribution of haplotypes was strongly influenced by limited dispersal distances, with the more recently derived haplotypes having much lower levels of dispersion and lower frequencies in populations than the ancestral haplotypes. The patterns of clade and haplotype dispersion and displacement and the distribution of morphotypes imply at least three cases of long-distance dispersal and one case of historical fragmentation. The historical patterns inferred for populations of Piriqueta are consistent with known biogeographical events, historical vegetation change, and the concordant patterns of multiple Pleistocene refugia that have been observed for a number of other taxa in southeastern North America.     

Ecological diversity and speciation in land snails of the genus Mandarina from the Bonin Islands

 Endemic land snails of the genus Mandarina of the oceanic Bonin Islands offer an example of habitat and character divergence among closely related species. The molecular phylogenies of Mandarina show that a divergence of arboreal, semiarboreal, and ground-dwelling species has occurred repeatedly in different times, areas, and lineages. Ecological diversification is suggested to be important for the coexistence of Mandarina species based on the facts that sympatric species are typically highly differentiated ecologically and morphologically, and that species occupying similar habitats do not coexist. The ecological diversification of Mandarina has occurred without much genetic divergence compared with that of its mainland relatives. This suggests that morphological and ecological diversifications are accelerated in depauperate environments where there are fewer competitors and predators. Although the details of the reproductive isolation mechanisms are not understood and further examination is needed, the rapid evolution of prezygotic isolation is the main cause of speciation in Mandarina. In particular, ecological diversification may be an effective barrier to gene exchange between two species. Because of incomplete postmating isolation and the lower genetic divergence among species of Mandarina, breakdowns of reproductive isolation have frequently occurred as a result of habitat change. It is important to estimate the effect of hybridization on species diversification in future studies. Received: February 7, 2002 / Accepted: October 22, 2002 Acknowledgments I express my sincere thanks to A. Davison, B.C. Clarke, A. Guiller, D. Thomaz, K. Tomiyama, I. Hayami, and K. Tanabe for helpful advice and assistance. This study was supported by grants from the Japan Society for the Promotion of Science and the Nippon Life Insurance Foundation.     

Ecological reproductive isolation of coast and inland races of Mimulus guttatus

Adaptive divergence due to habitat differences is thought to play a major role in formation of new species. However it is rarely clear the extent to which individual reproductive isolating barriers related to habitat differentiation contribute to total isolation. Furthermore, it is often difficult to determine the specific environmental variables that drive the evolution of those ecological barriers, and the geographic scale at which habitat-mediated speciation occurs. Here, we address these questions through an analysis of the population structure and reproductive isolation between coastal perennial and inland annual forms of the yellow monkeyflower, Mimulus guttatus. We found substantial morphological and molecular genetic divergence among populations derived from coast and inland habitats. Reciprocal transplant experiments revealed nearly complete reproductive isolation between coast and inland populations mediated by selection against immigrants and flowering time differences, but not postzygotic isolation. Our results suggest that selection against immigrants is a function of adaptations to seasonal drought in inland habitat and to year round soil moisture and salt spray in coastal habitat. We conclude that the coast and inland populations collectively comprise distinct ecological races. Overall, this study suggests that adaptations to widespread habitats can lead to the formation of reproductively isolated species.     

Are the native giant tortoises from the Seychelles really extinct? A genetic perspective based on mtDNA and microsatellite data

The extinction of the giant tortoises of the Seychelles Archipelago has long been suspected but is not beyond doubt. A recent morphological study of the giant tortoises of the western Indian Ocean concluded that specimens of two native Seychelles species survive in captivity today alongside giant tortoises of Aldabra, which are numerous in zoos as well as in the wild. This claim has been controversial because some of the morphological characters used to identify these species, several measures of carapace morphology, are reputed to be quite sensitive to captive conditions. Nonetheless, the potential survival of giant tortoise species previously thought extinct presents an exciting scenario for conservation. We used mitochondrial DNA sequences and nuclear microsatellites to examine the validity of the rediscovered species of Seychelles giant tortoises. Our results indicate that the morphotypes suspected to represent Seychelles species do not show levels of variation and genetic structuring consistent with long periods of reproductive isolation. We found no variation in the mitochondrial control region among 55 individuals examined and no genetic structuring in eight microsatellite loci, pointing to the survival of just a single lineage of Indian Ocean tortoises.     

Genetic and morphological evidence for reproductive isolation between sympatric populations of Galaxias (Teleostei: Galaxiidae) in South Island, New Zealand

New Zealand's South Island houses a flock of closely related stream-resident fish taxa (Galaxias vulgaris sensu lato), including a number of species recently described on the basis of subtle morphological differences. The taxonomic status of some members of the species complex remains uncertain. This study examines the degree of reproductive isolation between recently recognized morphotypes from Southland (G. 'southern', flatheads; G. gollumoides, roundheads) which co-occur in Bushy Creek, a tributary of the Mataura R. Although these morphotypes are broadly sympatric in Southland and Stewart Island, Bushy Creek is their only documented zone of contact. Molecular (microsatellite, isozyme and mtDNA markers) and morphological analyses of 139 fish samples across a 500-m transect (seven stations) reveal a cline from predominantly G. 'southern' (N=85) to predominantly G. gollumoides (JV=54), corresponding with a gradual increase in stream gradient. Multivariate analyses of genotypic and morphological data independently reveal distinct clusters that are completely congruent with mtDNA type, suggesting an absence of mtDNA introgression. Our data support the separate species status of G. 'southern' and G. gollumoides under both biological and phylogenetic species concepts. We suggest that the speciation of these taxa occurred in allopatry through independent losses of diadromy, with sympatry resulting from secondary contact.     

Genetic divergence among morphotypes of Lake Tana (Ethiopia) barbs

The genus Barbus is a paraphyletic assemblage that includes three different ploidy levels: diploid, tetraploid and hexaploid. 'B.' intermedins , which inhabits Lake Tana (Ethiopia), is a hexaploid taxon that forms a 'species flock' consisting of at least 14 morphotypes. Thirty-one presumptive allozymic loci were analysed in a large sample of 'B.' intermedius. No diagnostic loci were observed between the morphotypes, but substantial differences in allele frequencies were found. One morphotype, Acute, differs significantly from the others. The presence of this genetic differentiation within the lake strongly suggests that the morphotypes are diverging lineages. Because of some parallel characteristics with cichlid species flocks, we put forward the hypothesis that the morphotypes of barbs in Lake Tana represent a species flock that originated via sympatric speciation with more rapid morphological than molecular differentiation. If the differentiation and the reproductive isolation are real, it is probable that the morphotypes already are or will soon reach the status of species.     

Island isolation and habitat heterogeneity correlate with DNA variation in a marine snail (Littorina saxatilis)

The null assumption of molecular variation is that most of it is neutral to natural selection. This is in contrast to variation in morphological traits that we generally assume is maintained by selection, and therefore often by selection coupled to environmental heterogeneity in time and space. Examples of molecular variation that vary over habitat-shifts, particularly in allozymes, show that the relative impact of non-neutral variation as compared to neutral variation might be substantial in some systems. To assess the importance of habitat-generated variation in relation to variation generated by random processes in nuclear DNA markers at small spatial scales, we compared the effects of island isolation and habitat heterogeneity on genetic substructuring in a rocky shore snail ( Littorina saxatilis ). This species has a restricted migration among islands owing to the lack of free-floating larvae. Earlier studies show that allozymes vary extensively as a consequence of isolation by water barriers among islands, but also as a consequence of divergent selection among different microhabitats within islands. In the DNA markers we observed genetic differentiation owing to island isolation at three of nine loci. In addition, variation at three loci correlated with habitat type, but the correlation for two of the loci was weak. Overall, isolation contributed slightly more to the genetic variation among populations than did habitat-related factors but the difference was small. It is concluded that both island isolation, which interrupts gene flow, and a heterogeneous habitat cause genetic substructuring at the DNA level in L. saxatilis in the studied area, and thus in this species we need to be somewhat concerned about habitat heterogeneity also at DNA loci.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 377–384.     

SpedeSTEM: a rapid and accurate method for species delimitation

We describe a software package (SpedeSTEM) that allows researchers to conduct a species delimitation analysis using intraspecific genetic data. Our method operates under the assumption that a priori information regarding group membership is available, for example that samples are drawn from some number of described subspecies, races or distinct morphotypes. SpedeSTEM proceeds by calculating the maximum likelihood species tree from all hierarchical arrangements of the sampled alleles and uses information theory to quantify the model probability of each permutation. SpedeSTEM is tested here against empirical and simulated data; results indicate that evolutionary lineages that diverged as few as 0.5N generations in the past can be validated as distinct using sequence data from little as five loci. This work enables speciation investigations to identify lineages that are evolutionarily distinct and thus have the potential to form new species before these lineages acquire secondary characteristics such as reproductive isolation or morphological differentiation that are commonly used to define species.     

Sympatric serpentine endemic Monardella (Lamiaceae) species maintain habitat differences despite hybridization

Ecological differentiation and genetic isolation are thought to be critical in facilitating coexistence between related species, but the relative importance of these phenomena and the interactions between them are not well understood. Here, we examine divergence in abiotic habitat affinity and the extent of hybridization and introgression between two rare species of Monardella (Lamiaceae) that are both restricted to the same serpentine soil exposure in California. Although broadly sympatric, they are found in microhabitats that differ consistently in soil chemistry, slope, rockiness and vegetation. We identify one active hybrid zone at a site with intermediate soil and above‐ground characteristics, and we document admixture patterns indicative of extensive and asymmetric introgression from one species into the other. We find that genetic distance among heterospecific populations is related to geographic distance, such that the extent of apparent introgression is partly explained by the spatial proximity to the hybrid zone. Our work shows that plant species can maintain morphological and ecological integrity in the face of weak genetic isolation, intermediate habitats can facilitate the establishment of hybrids, and that the degree of apparent introgression a population experiences is related to its geographic location rather than its local habitat characteristics.     

Geographic patterns of morphological variation in Turnera sidoides subsp. pinnatifida (Turneraceae)

With the objective of contributing to understanding the patterns of variation within the Turnera sidoides complex, a detailed evaluation of morphological variation along the range of T. sidoides subsp. pinnatifida was performed. A multivariate analysis based on leaf traits and flower colour data enabled differentiation of five morphotypes. Common-garden experiments demonstrated that the morphological variants have a strong genetic basis. It was also found that the morphotypes are geographically structured along the subspecies range, display different habitat preferences, and occur in regions with different climatic regimes. Although these results are suggestive of adaptive differentiation of T. sidoides subsp. pinnatifida, comparisons between morphological and bioclimatic ordinations showed that the patterns observed cannot be fully explained by current climatic conditions. It is proposed that Miocene–Pleistocene events may explain the origin of the five morphotypes and that current climatic and ecological factors may be contributing to the maintenance of the extent and patterns of morphological differentiation in T. sidoides subsp. pinnatifida.