The allopatric phase of speciation: the sharp-beaked ground finch (Geospiza difficilis) on the Galápagos islands

Using microsatellite DNA variation, morphological measurements and sonagrams made from tape-recordings in the field, we examine die allopatric differentiation of six populations of the sharp-beaked ground finch, Geospiza difficilis , in the Galapagos archipelago. We ask how and why die populations became differentiated, and consider what die differences imply about speciation. An important factor is time; G. difficilis is one of the phylogenetically oldest species. Populations became differentiated by adapting in beak morphology to different food supplies. Since beak size and shape also function in conspecific mate recognition and choice, die potential for reproductive isolation from sister and parental taxa arose as a correlated effect of natural selection on resource-exploiting traits. This conforms to a standard explanation for the origin of pre-mating isolation as a byproduct of adaptive changes in allopatry without being adaptive itself. However, diis explanation is incomplete. Vocal characteristics also differentiated, partly as a result of natural and sexual selection independent of beak size change in environments with different sound transmitting properties. An additional element of chance is indicated by a comparison of closely-related populations on two islands, Wolf and Darwin, that are geographically close, and topographically and floristically similar. The populations have markedly different vocalizations. Morphological characters, vocalizations and genetic traits do not vary concordandy among die six populations. One population (Genovesa) is genetically more similar to other congeneric species. Phenotypic similarities with G. difficilis are the result of a uniquely long retention of shared ancestral traits. Arguments under the phylogenetic species concept justify recognizing this population as a separate species, Geospiza acutirostris. Under the biological species concept it should remain as currentiy classified, G. difficilis.     

Hybridization masks speciation in the evolutionary history of the Galápagos marine iguana

The effects of the direct interaction between hybridization and speciation—two major contrasting evolutionary processes—are poorly understood. We present here the evolutionary history of the Galápagos marine iguana (Amblyrhynchus cristatus) and reveal a case of incipient within-island speciation, which is paralleled by between-island hybridization. In-depth genome-wide analyses suggest that Amblyrhynchus diverged from its sister group, the Galápagos land iguanas, around 4.5 million years ago (Ma), but divergence among extant populations is exceedingly young (less than 50 000 years). Despite Amblyrhynchus appearing as a single long-branch species phylogenetically, we find strong population structure between islands, and one case of incipient speciation of sister lineages within the same island—ostensibly initiated by volcanic events. Hybridization between both lineages is exceedingly rare, yet frequent hybridization with migrants from nearby islands is evident. The contemporary snapshot provided by highly variable markers indicates that speciation events may have occurred throughout the evolutionary history of marine iguanas, though these events are not visible in the deeper phylogenetic trees. We hypothesize that the observed interplay of speciation and hybridization might be a mechanism by which local adaptations, generated by incipient speciation, can be absorbed into a common gene pool, thereby enhancing the evolutionary potential of the species as a whole.     

Population genetics of Galápagos land iguana (genus Conolophus) remnant populations

The Galápagos land iguanas (genus Conolophus) have faced significant anthropogenic disturbances since the 17th century, leading to severe reduction of some populations and the extinction of others. Conservation activities, including the repatriation of captive‐bred animals to depleted areas, have been ongoing since the late 1970s, but genetic information has not been extensively incorporated. Here we use nine species‐specific microsatellite loci of 703 land iguanas from the six islands where the species occur today to characterize the genetic diversity within, and the levels of genetic differentiation among, current populations as well as test previous hypotheses about accidental translocations associated with early conservation efforts. Our analyses indicate that (i) five populations of iguanas represent distinct conservation units (one of them being the recently discovered rosada form) and could warrant species status, (ii) some individuals from North Seymour previously assumed to be from the natural Baltra population appear related to both Isabela and Santa Cruz populations, and (iii) the five different management units exhibit considerably different levels of intrapopulation genetic diversity, with the Plaza Sur and Santa Fe populations particularly low. Although the initial captive breeding programmes, coupled with intensive efforts to eradicate introduced species, saved several land iguana populations from extinction, our molecular results provide objective data for improving continuing in situ species survival plans and population management for this spectacular and emblematic reptile.     

Development of primers to characterize the mitochondrial control region of Galápagos land and marine iguanas (Conolophus and Amblyrhynchus)

Primers were developed for the amplification and sequencing of the mitochondrial control region of Galápagos land (Conolophus) and marine (Amblyrhynchus) iguanas. Sequences were obtained for four land iguana samples from two islands and for 28 marine iguana samples from three islands. A series of 70–80 bp tandem repeats adjacent to the control region are described and preliminary quantification of intra‐ and interspecific sequence divergence is included.     

Reproductive cycles and reproductive strategies among populations of the Rose‐bellied Lizard Sceloporus variabilis (Squamata: Phrynosomatidae) from central Mexico

Species with wide distribution, generally show variations in life history characteristics, which can be attributed to environmental causes. In this study, we analyzed the reproductive cycle and reproductive characteristics from three populations (Atlapexco, San Pablo Tetlapayac, and Santa Catarina) of the lizard Sceloporus variabilis from central Mexico. The specific goal of this study was to evaluate life history characteristics such as reproductive period extent, SVL (snout‐vent length) at sexual maturity, clutch size, egg mass and volume, and RCM (relative clutch mass). The San Pablo Tetlapayac population showed a larger clutch size, RCM, egg mass, and a smaller SVL, body mass and reproductive period (January‐September), as well as egg volume than the Atlapexco and Santa Catarina populations. Reproductive cycle and reproductive characteristics were more similar between the Atlapexco and Santa Catarina populations. Differences found in the population of San Pablo Tetlapayac with respect to the Atlapexco and Santa Catarina populations could be attributed to environmental variations where lizard populations occur. Differences in the reproductive period and reproductive characteristics in each population could be the result of both historical (phylogenetic; e.g., reproductive mode) and nonhistorical (environmental; e.g., temperature, food availability) causes. This study showed that populations of the same species are under different selection pressures, and these affect the reproductive characteristics of populations. Our results also indicate that long‐term and targeted studies on predation, use and selection of food, are needed to determine the causes of these variations in populations of S. variabilis.     

Phylogenetic community ecology and the role of social dominance in sponge-dwelling shrimp

When functional traits are evolutionarily conserved, phylogenetic relatedness can serve as a proxy for ecological similarity to examine whether functional differences among species mediate community assembly. Using phylogenetic- and trait-based analyses, we demonstrate that sponge-dwelling shrimp (Synalpheus) assemblages are structured by size-based habitat filtering, interacting with competitive exclusion mediated by social system. Most shrimp communities were more closely related and/or more similar in size than randomized communities, consistent with habitat filtering facilitated by phylogenetically conserved body size. Those sponges with greater space heterogeneity hosted shrimp communities with greater size diversity, corroborating the importance of size in niche use. However, communities containing eusocial shrimp - which cooperatively defend territories - were less phylogenetically related and less similar in size, suggesting that eusociality enhances competitive ability and drives competitive exclusion. Our analyses demonstrate that community assembly in this diverse system occurs via traits mediating niche use and differential competitive ability.     

Comparing phylogenetic signal in intraspecific and interspecific body size datasets

Phylogenetic comparative methods have become a standard statistical approach for analysing interspecific data, under the assumption that traits of species are more similar than expected by chance (i.e. phylogenetic signal is present). Here I test for phylogenetic signal in intraspecific body size datasets to evaluate whether intraspecific datasets may require phylogenetic analysis. I also compare amounts of phylogenetic signal in intraspecific and interspecific body size datasets. Some intraspecific body size datasets contain significant phylogenetic signal. Detection of significant phylogenetic signal was dependant upon the number of populations (n) and the amount of phylogenetic signal (K) for a given dataset. Amounts of phylogenetic signal do not differ between intraspecific and interspecific datasets. Further, relationships between significance of phylogenetic signal and sample size and amount of phylogenetic signal are similar for intraspecific and interspecific datasets. Thus, intraspecific body size datasets are similar to interspecific body size datasets with respect to phylogenetic signal. Whether these results are general for all characters requires further study.     

Genetic impact of a severe El Niño event on Galápagos marine iguanas (Amblyrhynchus cristatus)

The El Niño-Southern Oscillation (ENSO) is a major source of climatic disturbance, impacting the dynamics of ecosystems worldwide. Recent models predict that human-generated rises in green-house gas levels will cause an increase in the strength and frequency of El Niño warming events in the next several decades, highlighting the need to understand the potential biological consequences of increased ENSO activity. Studies have focused on the ecological and demographic implications of El Niño in a range of organisms, but there have been few systematic attempts to measure the impact of these processes on genetic diversity in populations. Here, we evaluate whether the 1997–1998 El Niño altered the genetic composition of Galápagos marine iguana populations from eleven islands, some of which experienced mortality rates of up to 90% as a result of El Niño warming. Specifically, we measured the temporal variation in microsatellite allele frequencies and mitochondrial DNA diversity (mtDNA) in samples collected before (1991/1993) and after (2004) the El Niño event. Based on microsatellite data, only one island (Marchena) showed signatures of a genetic bottleneck, where the harmonic mean of the effective population size (N_e) was estimated to be less than 50 individuals during the period between samplings. Substantial decreases in mtDNA variation between time points were observed in populations from just two islands (Marchena and Genovesa). Our results suggests that, for the majority of islands, a single, intense El Niño event did not reduce marine iguana populations to the point where substantial neutral genetic diversity was lost. In the case of Marchena, simultaneous changes to both nuclear and mitochondrial DNA variation may also be the result of a volcanic eruption on the island in 1991. Therefore, studies that seek to evaluate the genetic impact of El Niño must also consider the confounding or potentially synergistic effect of other environmental and biological forces shaping populations.     

Longitudinal gradients in the phylogenetic community structure of European Tenebrionidae (Coleoptera) do not coincide with the major routes of postglacial colonization

Species specific colonization abilities and biotic and abiotic filters influence the local and regional faunal composition along colonization trajectories. Using a recent compilation of the occurrences of 1373 darkling beetle (Tenebrionidae) species and subspecies in 49 European countries and major islands, we reconstructed the tenebrionid postglacial colonization of middle and northern Europe from southern European glacial refuges and linked species composition to latitudinal and longitudinal gradients in phylogenetic relatedness across Europe. The majority of European islands and mainland countries appeared to be phylogenetically clustered. We did not find significant latitudinal trends in average phylogenetic relatedness of regional faunas along the supposed postglacial colonization routes but detected a strong positive correlation between mean relatedness and longitude of mainland faunas and an opposite negative correlation for island faunas. The strength of phylogenetic relatedness in the regional tenebrionid faunas decreased significantly with latitude and to a lesser degree with longitude. These findings are in accordance with two trajectories of postglacial colonization from centres in Spain and middle Asia that caused a strong longitudinal trend in the phylogenetic relatedness. Subsequent pair‐wise analyses of species co‐occurrences showed that species of similar distributional ranges tend to be phylogenetically clustered and species of different spatial distribution to be phylogenetically segregated. Both findings are in accordance with the concept of ‘range size heritability’. Our study demonstrates that taxonomic data are sufficiently powerful to infer continental wide patterns in phylogenetic relatedness that can be linked to colonization history and geographic information.     

Phylogeography of the endemic St. Lucia whiptail lizard Cnemidophorus vanzoi: Conservation genetics at the species boundary

Vicariance and isolation leading to speciation of reptiles on islands is well exemplified in a number of taxa in the Caribbean. The St. Lucia whiptail (Cnemidophorus vanzoi), considered a single species, is found on two small islets (Maria Major and Maria Minor) off the main island of St. Lucia. From lizards collected from both localities, we gathered morphological measurements and analysed the genetic divergence between populations, using a molecular survey of ∼ ∼2800 mtDNA base pairs and 8 microsatellites. There are significant differences in body size and general form and fixed but small mtDNA differences between island populations. Microsatellites reveal low diversity within populations but very high differentiation between islands with non-overlapping allele size ranges at all except one microsatellite and two loci exhibiting single-base polymorphism, fixed between islands. Based on these results, we examine published criteria to determine whether the studied island forms could be considered true species. According to the phylogenetic species concept and Moritz’s evolutionary significant unit (ESU) criteria, the two lizard populations can be considered separate entities. Crandall et al.’s (2000, Trends Ecol. Evol., 15, 290–295) broader categorization of population distinctiveness, based on concepts of ecological and genetic exchangeability, produces conflicting results depending on the interpretation of the observed ecological data. Following Fraser and Bernatchez’s (2001, Mol. Ecol., 10, 2741–2752) framework for management decisions when ecological data are not sufficient we propose that the lizard populations on the Maria islands are on differing evolutionary trajectories and thus at the species boundary. The populations are of high priority to conservation, thus meriting separate management.     

The recent history and population structure of five Mandarina snail species from subtropical Ogasawara (Bonin Islands, Japan)

The effect of Pleistocene climate change on the organisms of tropical and subtropical regions is rather poorly understood. We therefore studied the land snail genus Mandarina (Bradybaenidae) of oceanic Ogasawara (Bonin Islands, Japan), with the aim of using population genetic data to understand their recent history. Our analysis of a mitochondrial 16S ribosomal RNA region from more than 600 snails in five ground-living species suggests that populations on the small islands of Mukoujima, Anejima, Imotojima and Meijima, as well as on the low-lying southern and central parts of Hahajima, have probably undergone recent bottlenecks followed by subsequent expansions. Except between the main island of Hahajima and Mukouijima, there is almost no evidence for gene flow among islands even though the islands were connected repeatedly by land bridges through the Pleistocene. Within islands the population structure is severe, suggestive of a long-term, low level of gene flow (F(ST) is frequently greater than 0.5 among geographically close populations). Finally, there is a marked genetic patchiness, meaning that genetically close populations are sometimes separated by genetically distant populations. These patterns could be a consequence of expansion from bottlenecks, low active dispersal and founder effects caused by rare long-distance migrants. Unfortunately, the exact nature of the refugia and bottlenecks remains unknown because the palaeoclimate of this region is poorly understood. Dating the population size changes is also challenging because the molecular clock is uncertain. We suggest, however, that arid conditions or deforestation induced by decreased atmospheric CO(2) may have been the main factor in determining population size.     

Of mice and mammoths: evaluations of causal explanations for body size evolution in insular mammals

Aim We investigated the hypothesis that the insular body size of mammals results from selective forces whose influence varies with characteristics of the focal islands and the focal species, and with interactions among species (ecological displacement and release). Location Islands world‐wide. Methods We assembled data on the geographic characteristics (area, isolation, maximum elevation, latitude) and climate (annual averages and seasonality of temperature and precipitation) of islands, and on the ecological and morphological characteristics of focal species (number of mammalian competitors and predators, diet, body size of mainland reference populations) that were most relevant to our hypothesis (385 insular populations from 98 species of extant, non‐volant mammals across 248 islands). We used regression tree analyses to examine the hypothesized contextual importance of these factors in explaining variation in the insular body size of mammals. Results The results of regression tree analyses were consistent with predictions based on hypotheses of ecological release (more pronounced changes in body size on islands lacking mammalian competitors or predators), immigrant selection (more pronounced gigantism in small species inhabiting more isolated islands), thermoregulation and endurance during periods of climatic or environmental stress (more pronounced gigantism of small mammals on islands of higher latitudes or on those with colder and more seasonal climates), and resource subsidies (larger body size for mammals that utilize aquatic prey). The results, however, were not consistent with a prediction based on resource limitation and island area; that is, the insular body size of large mammals was not positively correlated with island area. Main conclusions These results support the hypothesis that the body size evolution of insular mammals is influenced by a combination of selective forces whose relative importance and nature of influence are contextual. While there may exist a theoretical optimal body size for mammals in general, the optimum for a particular insular population varies in a predictable manner with characteristics of the islands and the species, and with interactions among species. This study did, however, produce some unanticipated results that merit further study – patterns associated with Bergmann’s rule are amplified on islands, and the body size of small mammals appears to peak at intermediate and not maximum values of latitude and island isolation.     

Enhanced colour polymorphisms in island populations of the land snail Euhadra peliomphala

Variations in visible genetic polymorphisms are assumed to decrease in populations on small islands because of intense founder effects, genetic drift and inbreeding. However, we have found evidence of a marked enhancement of colour polymorphisms within populations on small oceanic islands that were colonized from the mainland. The source populations on the mainland of the land snail Euhadra peliomphala in four oceanic islands were estimated by phylogenetic analysis of mitochondrial DNA sequences. Diversity of shell colour was higher in the island populations than in the source populations on the mainland. In addition, the shell colour morphs differed not only among populations from different islands but also between the island populations and the source populations on the mainland. By contrast, no mtDNA variations were found in any of the island populations, even though the source populations possessed high mtDNA diversity. Thus, components of colour morphs changed in the island populations after their colonization, and colour polymorphisms are enhanced in these islands despite the loss of genetic variation. The above findings suggest that ecological mechanisms such as morphological release owing to a release from competition may overcome the tendency toward reduced genetic variation in islands to enhance the colour polymorphism.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 417–425.     

Reed frog diversification in the Gulf of Guinea: Overseas dispersal,the progression rule,and in situ speciation

Oceanic islands accumulate endemic species when new colonists diverge from source populations or by in situ diversification of resident island endemics. The relative importance of dispersal versus in situ speciation in generating diversity on islands varies with a number of archipelago characteristics including island size, age, and remoteness. Here, we characterize interisland dispersal and in situ speciation in frogs endemic to the Gulf of Guinea islands. Using mitochondrial sequence and genome‐wide single‐nucleotide polymorphism data, we demonstrate that dispersal proceeded from the younger island (São Tomé) to the older island (Príncipe) indicating that for organisms that disperse overseas on rafts, dispersal between islands may be determined by ocean currents and not island age. We find that dispersal between the islands is not ongoing, resulting in genotypically distinct but phenotypically similar lineages on the two islands. Finally, we demonstrate that in situ diversification on São Tomé Island likely proceeded in allopatry due to the geographic separation of breeding sites, resulting in phenotypically distinct species. We find evidence of hybridization between the species where their ranges are sympatric and the hybrid zone coincides with a transition from agricultural land to primary forest, indicating that anthropogenic development may have facilitated secondary contact between previously allopatric species.     

Host islands within the California Northern Channel Islands create fine-scale genetic structure in two sympatric species of the symbiotic ectomycorrhizal fungus Rhizopogon

We have examined fine-scale genetic structure of the symbiotic ectomycorrhizal fungi Rhizopogon occidentalis and R. vulgaris on two of the California Channel Islands using five and six microsatellite loci, respectively. Both Rhizopogon species are sympatric on Santa Cruz and Santa Rosa Islands and are ectomycorrhizal with bishop pine (Pinus muricata) on both islands or Santa Rosa Island Torrey pine (P. torreyana ssp. insularis) on Santa Rosa. The combination of disjunct pine host distributions and geographic barriers within and among the islands have created highly structured Rhizopogon populations over very short distances (8.5 km on Santa Cruz Island; F(ST) = 0.258, F(ST) = 0.056, R. occidentalis and R. vulgaris, respectively). Both species show similar patterns of genetic differentiation as a result of limited dispersal between host populations as revealed by a significant isolation by distance relationship (r = 0.69, P < 0.04; r = 0.93, P < 0.001, R. occidentalis and R. vulgaris, respectively) and Bayesian clustering analyses, and is most likely a function of the small foraging range of the few mammals that disperse Rhizopogon on these islands and the enormous spore bank characteristic of Rhizopogon species.     

Distribution and phylogenetic analyses of an endangered tick,Amblyomma sphenodonti

Abstract

In this study we investigate the geographic distribution, genetic diversity, and phylogenetic relationships of an endangered tick, Amblyomma sphenodonti (Family Ixodidae). Amblyomma sphenodonti and its host, the tuatara (Sphenodon), are found only on small offshore islands around New Zealand. Our results show that Amblyomma sphenodonti has a more severely restricted geographic distribution than its host, as it was found on only eight of 28 islands (four out of 12 island groups) where tuatara still live. The prevalence of A. sphenodonti is likely to have been affected by low host density and fluctuations in host population size as tuatara populations became isolated on offshore islands. Analysis of A. sphenodonti cytochrome oxidase 1 (CO1) sequences indicated a lack of gene flow between islands, with fixed differences in CO1 sequences between islands, but almost no genetic diversity within island populations. A similar phylogenetic pattern to that observed in tuatara mtDNA was observed, indicating co‐evolution of two species, at least since the Pleistocene. Phylogenetic analysis using 18S rRNA sequences suggest that A. sphenodonti is not closely related to other Amblyomma species, and that a separate genus for this species may be warranted. However, data from other ixodid ticks are required before the distinctiveness of A. sphenodonti can be confirmed and the phylogenetic relationships among ixodid ticks fully understood.     

Exploring the Phylogenetic Structure of Ecological Communities: An Example for Rain Forest Trees

Because of the correlation expected between the phylogenetic relatedness of two taxa and their net ecological similarity, a measure of the overall phylogenetic relatedness of a community of interacting organisms can be used to investigate the contemporary ecological processes that structure community composition. I describe two indices that use the number of nodes that separate taxa on a phylogeny as a measure of their phylogenetic relatedness. As an example of the use of these indices in community analysis, I compared the mean observed net relatedness of trees (>/=10 cm diameter at breast height) in each of 28 plots (each 0.16 ha) in a Bornean rain forest with the net relatedness expected if species were drawn randomly from the species pool (of the 324 species in the 28 plots), using a supertree that I assembled from published sources. I found that the species in plots were more phylogenetically related than expected by chance, a result that was insensitive to various modifications to the basic methodology. I tentatively infer that variation in habitat among plots causes ecologically more similar species to co-occur within plots. Finally, I suggest a range of applications for phylogenetic relatedness measures in community analysis.     

Inter-population variation of carotenoids in Galápagos land iguanas (Conolophus subcristatus)

Carotenoids have received much attention from biologists because of their ecological and evolutionary implications in vertebrate biology. We sampled Galápagos land iguanas (Conolophus subcristatus) to investigate the types and levels of blood carotenoids and the possible factors affecting inter-population variation. Blood samples were collected from populations from three islands within the species natural range (Santa Cruz, Isabela, and Fernandina) and one translocated population (Venecia). Lutein and zeaxanthin were the predominant carotenoids found in the serum. In addition, two metabolically modified carotenoids (anhydrolutein and 3'-dehydrolutein) were also identified. Differences in the carotenoid types were not related to sex or locality. Instead, carotenoid concentration varied across the localities, it was higher in females, and it was positively correlated to an index of body condition. Our results suggest a possible sex-related physiological role of xanthophylls in land iguanas. The variation in the overall carotenoid concentration between populations seems to be related to the differences in local abundance and type of food within and between islands.     

Ecological and morphological patterns in communities of land snails of the genus Mandarina from the Bonin Islands

The land snail genus Mandarina has undergone extensive radiation within the Bonin Islands in the west Pacific. The preferred above-ground vegetation heights of sympatric species were clearly different. They separated into arboreal, semi-arboreal, exposed ground and sheltered ground ecotypes. Shells of species with different ecotypes differ markedly, but shells of species with the same ecotype are very similar to each other. Shell morphologies of some phylogenetically distantly related species with the same ecotype were indistinguishable. Character evolution estimated parsimoniously using a phylogenetic tree suggests that the speciation among sympatric species is accompanied by ecological and morphological diversification. In addition, species coexistence of Mandarina is related to niche differentiation. The above findings suggest that ecological interactions among species contribute to the ecological and morphological diversification and radiation of these land snails in this depauperate environment.     

Disentangling the effects of intraspecies variability,phylogeny, space,and climate on the evolution of shell morphology in endemic Greek land snails of the genus Codringtonia

Extensive variation in land snail shell morphology has been widely documented, although few studies have attempted to investigate the ecological and evolutionary drivers of this variation. Within a comparative phylogenetic framework, we investigated the temporal and spatial evolution of the shell morphology of the Greek endemic land snail genus Codringtonia. The contribution of both inter‐ and intraspecies shell differentiation in the overall shell variability is assessed. The effect of climate, space, and evolutionary history on the shell variability was inferred using a variance partitioning framework. For Codringtonia species, intraspecies divergence of shell traits contributes substantially to the overall shell variability. By decomposing this variability, it was shown that the overall shell size of Codringtonia clades is phylogenetically constrained, related to early speciation events, and strongly affected by large‐scale spatial variability (latitudinal gradient). The effect of climate on shell size cannot be disentangled from phylogeny and space. Shell and, to a larger extent, aperture shape are not phylogenetically constrained, and appear to be mostly related to conspecific populations divergence events. Shell shape is substantially explained by both climate and space that greatly overlap. Aperture shape is mainly interpreted by medium to small‐scale spatial variables. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 796–813.