Evolutionary history of Cuban crocodiles Crocodylus rhombifer and Crocodylus acutus inferred from multilocus markers

Among crocodilians, Crocodylus rhombifer is one of the world's most endangered species with the smallest natural distribution. In Cuba, this endemic species coexists with the American crocodile (Crocodylus acutus). Hybridization between these two species is well known in captivity and might occur in the wild, but has never been demonstrated genetically. Here, we combined molecular data with environmental, geographic, and fossil data to infer the evolutionary history of Crocodylus in the Cuban Archipelago, and to evaluate genealogical support for species boundaries. We analyzed seven microsatellite loci plus DNA sequence data from nuclear (RAG-1) and mitochondrial (cytochrome b and cytochrome oxidase I) genes from 89 wild-caught individuals in Cuba, Grand Cayman Island, Jamaica, and Central America, and two samples from zoo collections. Microsatellites showed evidence of introgression, suggesting potential hybridization among Cuban groups. In Cuba, C. acutus contained one mitochondrial DNA (mtDNA) haplotype, whereas C. rhombifer contained two haplotypes. MtDNA data showed that C. acutus is paraphyletic with respect to C. rhombifer, revealing 1% sequence divergence between species within Cuba vs. 8% divergence between Cuban forms and mainland C. acutus. We suggest that hybridization has been a historical as well as a current phenomenon between C. acutus and C. rhombifer. These findings suggest that long-term conservation of crocodiles in Cuba will require identification of genetically pure and hybrid individuals, and a decrease in anthropogenic activities. We also recommend more extensive morphological and genetic analyses of Cuban population to establish clear boundaries of the hybrid zone between C. acutus and C. rhombifer.     

HISTORICAL BIOGEOGRAPHY OF THE BANANAQUIT (COEREBA FLAVEOLA) IN THE CARIBBEAN REGION: A MITOCHONDRIAL DNA ASSESSMENT

We analyzed mitochondrial DNA (mtDNA) restriction-site variation in bananaquit (Coereba flaveola; Aves, Coerebinae) populations sampled on 12 Caribbean islands and at 5 continental localities in Central America and northern South America. Multiple fixed restriction-site differences genetically defined several regional bananaquit populations. An mtDNA clade representing all Jamaican bananaquits was the most divergent; the estimated average sequence divergence (d_xy) between Jamaican and all other mtDNA haplotypes surveyed was 0.027. Three groups of populations, representing Central America, northern South America, and the eastern Antilles (Puerto Rico to Grenada) were nearly equally differentiated among themselves (average d_xy = 0.014), and may represent a single, recent range expansion. Within the eastern Antilles, three geographically restricted haplotype groups were identified: Puerto Rico, north-central Lesser Antilles (U.S. Virgin Islands to St. Lucia), and Grenada–St. Vincent. The evolutionary relationships of these groups were not clear. Genetic homogeneity of the island populations from the U.S. Virgin Islands to St. Lucia suggested a recent spread of a specific north-central Lesser Antillean haplotype through most of those islands. Haplotype variation across this region indicated that this spread may have occurred in two waves, first through the southernmost islands of St. Lucia, Martinique, and Dominica, and more recently from Guadeloupe to the north. The geographic distribution of mtDNA haplotypes, and of bananaquit populations, suggests periods of invasiveness followed by relative geographic quiescence. Although most genetic studies of bird populations have revealed homogeneity over large geographic areas, our findings provide a remarkable counterexample of strong geographic structuring of mtDNA variation over relatively small distances. Furthermore, although the mtDNA data were consistent with several subspecific distinctions, it was clear that named subspecies do not define equally differentiated evolutionary entities.     

Genealogical concordance and the specific status of Peromyscus sejugis

Peromyscus sejugis, a peripheral isolate of Peromyscus maniculatus, is a threatened taxon endemic to 2 small islands in the Sea of Cortés. Although its insularity makes the specific recognition of P. sejugis inherently problematic, resolution of this problem has important conservation implications. To evaluate the specific validity and evolutionary history of P. sejugis, we compared sequence variation (ND3/ND4L/ND4) in mtDNA for both island populations of P. sejugis with that for 8 populations of P. maniculatus from mainland Baja California. Each island population of P. sejugis had a single haplotype (0.7% sequence divergence), whereas 11 different haplotypes (mean sequence divergence = 0.68%) were obtained for the populations of P. maniculatus. The mean sequence divergence between the populations of the 2 species was 2.0%. Nested clade analysis supports the conclusion that P. sejugis is an insular isolate of P. maniculatus from mainland Baja California. Although our analysis confirms a low level of mtDNA divergence between P. sejugis and P. maniculatus from Baja California, the genealogical concordance of morphological, chromosomal, microsatellite, and mtDNA haplotype distinctiveness supports the conclusion that the 2 island populations of P. sejugis constitute independent evolutionarily significant units and together represent a phylogenetic species distinct from the P. maniculatus from Baja California.     

Molecular and morphological support for a Florida origin of the Cuban oak

Aim The origins of the Cuban biota are of long‐standing interest in biogeography, and the source of a small live oak (Quercus series Virentes) population on Cuba remains unresolved. Based on morphological evidence, previous authors have hypothesized a Florida origin from either Q. geminata or Q. virginiana or both; a Mexican origin from Q. oleoides; or a hybrid origin from both sources. We use molecular data and taxonomically informative leaf morphology to identify the source species and timing of colonization. Location Cuba, Central America, Mexico and the south‐eastern United States. Methods  We collected representative samples of Cuban oaks and each putative source species and genotyped each sample at 12 nuclear microsatellites and two chloroplast DNA sequences. We estimated population structure using a Bayesian clustering analysis and F‐statistics, pairwise migration rates among taxa, and divergence time using an isolation‐with‐migration model. We measured seven leaf traits and conducted an analysis of similarity (ANOSIM) to determine which putative source species was most similar to Cuban oaks. Results Cuban oak contains one chloroplast DNA haplotype, which is common in southern Florida. Bayesian clustering analysis of microsatellites revealed that the Cuban oak forms a distinct and pure population cluster, and F‐statistics showed that Cuban oaks are differentiated least from Q. virginiana and most from Q. geminata. Migration rates were highest out of Cuba to Q. oleoides. Molecular diversity, the ratio of allelic richness to allele size range, and effective population size of the Cuban oak were relatively low, suggesting a founder effect. Divergence time estimates fell entirely within the Pleistocene (628–6 ka), considering a range of mutation rates and generation times. Cuban oaks were morphologically most similar to Q. virginiana and least similar to Q. geminata. Main conclusions Molecular and morphological data support a Pleistocene dispersal of Q. virginiana from Florida to Cuba, followed by isolation and divergence, then limited dispersal and introgression from Cuba to Q. oleoides in Central America. Birds could have dispersed acorns to Cuba during a glacial period when sea levels were low. These results highlight the varied origin of the Cuban biota and the possible role of Pleistocene glaciations in the establishment of temperate taxa in the tropics.     

MITOCHONDRIAL DNA SEQUENCE VARIATION AMONG NATURAL POPULATIONS OF THE TRINIDAD GUPPY,POECILIA RETICULATA

Guppies were sampled from eight populations representing four river drainage basins in northern Trinidad, and from one population on the nearby island of Tobago. For each individual, a 465 base pair (bp) segment of the control region of the mitochondrial genome was sequenced. The resulting DNA sequences were subjected to sequence divergence calculations and the populations were linked by maximum parsimony analysis to determine their phylogenetic relationships. Mitochondrial DNA (mtDNA) sequence variation was found both within and between river drainages, correlated with the geographic features of northern Trinidad. The variation observed exists primarily between drainages, particularly between the Oropuche drainage and all other Trinidad drainages examined. Estimates of time of divergence between guppy populations of different drainages, based on mtDNA sequence variation, ranged from 100,000 to 200,000 for the most recently separated populations and from 600,000 to 1.2 million years between the Oropuche populations and all others examined. Examination of fish from northeastern South America will be required to determine whether these populations differentiated in their present locations or were the result of separate invasions of Trinidad from different Venezuelan sources. However, genetic isolation of these populations appears to predate the current physical separation of the island of Trinidad from the Venezuelan mainland.     

Partial island submergence and speciation in an adaptive radiation: a multilocus analysis of the Cuban green anoles

Sympatric speciation is often proposed to account for species-rich adaptive radiations within lakes or islands, where barriers to gene flow or dispersal may be lacking. However, allopatric speciation may also occur in such situations, especially when ranges are fragmented by fluctuating water levels. We test the hypothesis that Miocene fragmentation of Cuba into three palaeo-archipelagos accompanied species-level divergence in the adaptive radiation of West Indian Anolis lizards. Analysis of morphology, mitochondrial DNA (mt DNA) and nuclear DNA in the Cuban green anoles (carolinensis subgroup) strongly supports three pre dictions made by this hypothesis. First, three geographical sets of populations, whose ranges correspond with palaeo-archipelago boundaries, are distinct and warrant recognition as independent evolutionary lineages or species. Coalescence of nuclear sequence fragments sampled from these species and the large divergences observed between their mtDNA haplotypes suggest separation prior to the subsequent unification of Cuba ca. 5 Myr ago. Second, molecular phylogenetic relationships among these species reflect historical geographical relationships rather than morphological similarity. Third, all three species remain distinct despite extensive geographical contact subsequent to island unification, occasional hybridization and introgression of mtDNA haplotypes. Allopatric speciation initiated during partial island submergence may play an important role in speciation during the adaptive radiation of Anolis lizards.     

Phylogenetic affinities and inter-island differentiation in the Vitelline Warbler Dendroica vitellina, a West Indian endemic

The Vitelline Warbler Dendroica vitellina is endemic to the Cayman Islands and Swan Islands in the West Indies. This study examined the phylogenetic affinities of the Vitelline Warbler and assessed mitochondrial differentiation among the three Cayman Island populations. Species-level phylogenetic analyses based on 3639 nucleotides of mitochondrial DNA (mtDNA) sequence were used to place the Vitelline Warbler in the larger Dendroica radiation. These analyses confirmed that the Vitelline Warbler is the sister taxon of the Prairie Warbler Dendroica discolor, a species that breeds in continental North America. The magnitude of mitochondrial differentiation between these sister taxa (2.4%) supports their current classification as separate taxonomic species. Additional comparisons based on the 1041-nucleotide NDII gene sequence from 26 Vitelline Warblers provided evidence of within-species genetic structure. NDII haplotypes from Grand Cayman vs. Cayman Brac/Little Cayman differed by 6–10 nucleotide substitutions, and no haplotypes were shared among these island groups, supporting the current separation of the Cayman Island populations into two subspecies. These patterns support the biogeographical scenario that the Vitelline Warbler was derived from a mainland population of the Prairie Warbler. This may have occurred due to a loss of migration in ancestral populations or from over-water dispersal of a mainland resident population.     

Evolutionary history of the synbranchid eels (Teleostei: Synbranchidae) in Central America and the Caribbean islands inferred from their molecular phylogeny

Swamp eels of the genera Synbranchus and Ophisternon are secondary freshwater fishes whose biogeography provides evidence of their long residence in Mesoamerica, while their impoverished species-level taxonomy might suggest a more recent diversification or a conservative morphology. We have inferred the phylogenetic relationships of Synbranchus marmoratus and Ophisternon aenigmaticum from 45 drainages throughout South, Central America, and Cuba based on mitochondrial genes (cytochrome b and ATPase 8/6). Phylogeographic analysis supported the monophyly of Mesoamerican O. aenigmaticum although our results suggest that S. marmoratus is not a monophyletic group. We found a evolutionary differentiated Synbranchus mtDNA lineage inhabiting Las Perlas islands (Pacific Panama) that appeared to be taxonomically distinct and separated for a long period of time from the main Synbranchus clade. Major synbranchid clades were also corroborated with the nuclear RAG-1 gene (1171-bp). Application of two fish-based mtDNA clocks (1.05-1.3% pairwise divergence/million year (Ma)), is in accordance with the Gondwanian origin suggested for the Synbranchidae. The mtDNA lineages exhibited a remarkable geographic structure in Central America suggesting that vicariance has most likely promoted the Synbranchus and Ophisternon mtDNA diversification. Although our data indicate the importance of the Pacific area in Synbranchus differentiation, the mtDNA divergence between South and Central American Synbranchus is too small to support Cretaceous colonization via the proto-Antillean bridge suggested by Rosen [Syst. Zool. 24 (1976) 431]. Instead, our phylogeographic results suggest that Ophisternon and Synbranchus mtDNA clades most likely colonized Central America during the Miocene (12.7-23Ma) prior the final closure of the Isthmus of Panama (3.3Ma).     

Evolutionary history of the genus Rhamdia (Teleostei: Pimelodidae) in Central America

We constructed phylogenetic hypotheses for Mesoamerican Rhamdia, the only genus of primary freshwater fish represented by sympatric species across Central America. Phylogenetic relationships were inferred from analysis of 1990 base pairs (bp) of mitochondrial DNA (mtDNA), represented by the complete nucleotide sequences of the cytochrome b (cyt b) and the ATP synthase 8 and 6 (ATPase 8/6) genes. We sequenced 120 individuals from 53 drainages to provide a comprehensive geographic picture of Central American Rhamdia systematics and phylogeography. Phylogeographic analysis distinguished multiple Rhamdia mtDNA lineages, and the geographic congruence across evolutionarily independent Rhamdia clades indicated that vicariance has played a strong role in the Mesoamerican diversification of this genus. Phylogenetic analyses of species-level relationships provide strong support for the monophyly of a trans-Andean clade of three evolutionarily equivalent Rhamdia taxa: R. guatemalensis, R. laticauda, and R. cinerascens. Application of fish-based mitochondrial DNA clocks ticking at 1.3-1.5% sequence divergence per million years (Ma), suggests that the split between cis- and trans-Andean Rhamdia extends back about 8 Ma, and the three distinct trans-Andean Rhamdia clades split about 6 Ma ago. Thus the mtDNA divergence observed between cis- and trans-Andean Rhamdia species is too low to support an ancient colonization of Central America in the Late Cretaceous or Paleocene as had been hypothesized in one colonization model for Mesoamerican fishes. Rather the mtDNA data indicate that Rhamdia most likely colonized Central America in the late Miocene or Pliocene, promoting a strong role for the Isthmus of Panamá in the Mesoamerican expansion of this genus. Basal polytomies suggest that both the R. laticauda and R. guatemalensis clades spread rapidly across the Central American landscape, but differences in the average mtDNA genetic distances among clades comprising the two species, indicate that the R. laticauda spread and diversified across Mesoamerica about 1 million years before R. guatemalensis.     

Mainland colonization by island lizards

Aim We investigate biogeographic relationships within the lizard genus Anolis Daudin, 1802 to test the hypothesis that the mainland (Central and South American) Norops‐clade species descended from a West Indian Anolis ancestor. Previous hypotheses have suggested that close island relatives of mainland Norops species (the Cuban Anolis sagrei and Jamaican A. grahami series) represent over‐water dispersal from a mainland ancestor. These previous hypotheses predict that the A. sagrei and A. grahami series should be phylogenetically nested within a Norops clade whose ancestral geography traces to the mainland. If Norops is West Indian in origin, then West Indian species should span the deepest phylogenetic divergences within the Norops clade. Location Central and South America and West Indian islands. Methods The phylogenetic relationships of Anolis lizards are reconstructed from aligned DNA sequences using both parsimony and Bayesian approaches. Hypotheses are tested in two ways: (1) by reconstructing the ancestral geographic location for the Norops clade using Pagel & Lutzoni's (2002) Bayesian approach, and (2) by testing alternative topological arrangements via Wilcoxon Signed‐Ranks tests ( Templeton, 1983 ) and Shimodaira–Hasegawa tests ( Shimodaira & Hasegawa, 1999 ). Results Our evidence supports an origin of mainland Norops anoles from a West Indian ancestor. A West Indian ancestor to the Norops clade is statistically supported, and alternatives to the biogeographic pattern [Cuban (Jamaican, Mainland)] are statistically rejected by Shimodaira–Hasegawa tests, although not by Wilcoxon Signed‐Ranks tests. Main conclusions Our data support the hypothesis of a West Indian origin for mainland Norops. This result contradicts previous hypotheses and suggests that island forms may be an important source for mainland biodiversity.     

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.     

Scrophularia arguta,a widespread annual plant in the Canary Islands: a single recent colonization event or a more complex phylogeographic pattern?

Many studies have addressed evolution and phylogeography of plant taxa in oceanic islands, but have primarily focused on endemics because of the assumption that in widespread taxa the absence of morphological differentiation between island and mainland populations is due to recent colonization. In this paper, we studied the phylogeography of Scrophularia arguta, a widespread annual species, in an attempt to determine the number and spatiotemporal origins of dispersal events to Canary Islands. Four different regions, ITS and ETS from nDNA and psbA‐trnH and psbJ‐petA from cpDNA, were used to date divergence events within S. arguta lineages and determine the phylogenetic relationships among populations. A haplotype network was obtained to elucidate the phylogenetic relationships among haplotypes. Our results support an ancient origin of S. arguta (Miocene) with expansion and genetic differentiation in the Pliocene coinciding with the aridification of northern Africa and the formation of the Mediterranean climate. Indeed, results indicate for Canary Islands three different events of colonization, including two ancient events that probably happened in the Pliocene and have originated the genetically most divergent populations into this species and, interestingly, a recent third event of colonization of Gran Canaria from mainland instead from the closest islands (Tenerife or Fuerteventura). In spite of the great genetic divergence among populations, it has not implied any morphological variation. Our work highlights the importance of nonendemic species to the genetic richness and conservation of island flora and the significance of the island populations of widespread taxa in the global biodiversity.     

Climate‐mediated adaptation after mainland colonization of an ancestrally subtropical island lizard,Anolis carolinensis

Climate‐mediated evolution plays an integral role in species migration and range expansion. Gaining a clearer understanding of how climate affects demographic history and adaptation provides fundamental insight into the generation of intra‐ and interspecific diversity. In this study, we used the natural colonization of the green anole (Anolis carolinensis) from the island of Cuba to mainland North America to investigate the role of evolution at the niche, phenotypic and genetic levels after long‐term establishment in a novel environment. The North American green anole occupies a broader range of thermal habitats than its Cuban sister species. We documented niche expansion in the mainland green anole, mediated primarily through adaptation to winter temperatures. Common garden experiments strongly suggest a genetic component to differences in thermal performance found between populations in different temperature regimes. Analysis of geographic variation in population structure based on 53 486 single nucleotide variants from RAD loci revealed increased genetic isolation between populations in different vs. similar thermal environments. Selection scans for environment‐allele correlations reveal 19 genomic loci of known function that may have played a role in the physiological adaptation of A. carolinensis to temperate environments on the mainland.     

Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchuensis complex

Species whose geographical distribution encompasses both mainland and island populations provide an ideal system for examining isolation and genetic divergence. In this study, paternally transmitted chloroplast DNA (cpDNA) and maternally transmitted mitochondrial DNA (mtDNA) were used to estimate population structure and phylogeography of Pinus luchuensis, a species found in eastern China (ssp. hwangshanensis), Taiwan (ssp. taiwanensis), and the Ryukyu Archipelago (ssp. luchuensis). Gene genealogies of both mtDNA and cpDNA reveal two major lineages. Molecular dating indicates that these lineages diverged before the colonization of P. luchuensis subspecies in Taiwan and the Ryukyu Archipelago. Both mtDNA and cpDNA show a lack of correspondence between molecular phylogeny and subspecies designation. Phylogeographical analysis suggests that paraphyly of the subspecies is the result of recent divergence rather than secondary contacts. In spite of the short divergence history of P. luchuensis on islands, the island populations show the same degree of genetic divergence as mainland populations. Low levels of genetic diversity in the mainland ssp. hwangshanensis suggest demographic bottlenecks. In contrast, the high heterogeneity of genetic composition for island populations is likely to be associated with a history of multiple colonization from the mainland. The spatial apportionment of organelle DNA polymorphisms is consistent with a pattern of stepwise colonization on island populations.     

A phylogeny for grasshoppers of the genus Chitaura (Orthoptera: Acrididae) from Sulawesi, Indonesia, based on mitochondrial DNA sequence data

The Indonesian island of Sulawesi occupies a central position within the biogeographically complex region known as Wallacea. Its fauna is characterised by a high rate of endemism and a patchwork distribution of taxa within the island. The grasshopper genus Chitaura is a good example having at least ten endemic species with predominantly parapatric distributions. It can be used as a model for determining the origins of Sulawesi taxa and the within-island evolution that has led to the present patterns of distribution. Here we present a phylogenetic hypothesis for 28 individuals within the genus, including individuals of one species from Java and two from the Moluccas, based on DNA sequences of the mitochondrial cytochrome oxidase 1 gene. Frequent sequence heteroplasmy was observed. The phylogenetic hypothesis is consistent with recent interpretations of the geological history of Sulawesi suggesting separate evolution on the island for 7–14 Myr, possibly since South Sulawesi was connected to Borneo. Within the island, the pattern of genetic divergence is dominated by a strong correlation with geographic distance, with exceptions indicating past or present barriers to dispersal. Colonisation of the Moluccas from North or Central Sulawesi is implied. Levels of genetic divergence are compared with distribution patterns of colour morphs and with possible effects of tectonic movements in the Cenozoic, or Pleistocene climatic, vegetational and sea-level changes.     

Ancient differentiation in the single-island avian radiation of endemic Hispaniolan chat-tanagers (Aves: Calyptophilus)

The simple geographic structure of island systems often makes them tractable for studies of the patterns and processes of biological diversification. The Calyptophilus chat-tanagers of Hispaniola are of general evolutionary interest because their multiple lineages might have arisen on a single island, of conservation concern because several isolated populations are nearly extinct, and taxonomically ambiguous because they have been variously lumped or split into one to four species. To explore the context of diversification of the seven extant Calyptophilus populations, we conducted a multilocus coalescent analysis based on sequences of mitochondrial ND2 and three nuclear intron loci. We then compared patterns of phylogeographic genetic variation with the morphological differences that distinguish these populations. Mitochondrial haplotypes formed two reciprocally monophyletic groups separated by a large magnitude of nucleotide divergence. Intron structure largely paralleled the geographic grouping pattern of the mitochondrial DNA (mtDNA), but these groups were only reciprocally monophyletic at one of the three introns. Also, the magnitude of between-group divergence was much lower in the introns than mtDNA genealogies. Multilocus coalescent analyses inferred a nonzero divergence time between these two major geographic groups, but suggested that they have experienced a low level of gene flow. All four markers showed substantial allele sharing within each of the two groups, demonstrating that many now separated montane populations do not have long histories of isolation. Considered in concert, our multilocus phylogeographic reconstructions support the recognition of two species within the Calyptophilus complex, and raise the possibility that these taxa differentiated prior to the fusion of the two palaeo-islands that form present-day Hispaniola.     

Phylogeographic Patterns and Evolution of the Mitochondrial DNA Control Region in Two Neotropical Cats (Mammalia, Felidae)

The ocelot (Leopardus pardalis) and margay (L. wiedii) are sister-species of Neotropical cats which evolved from a lineage that migrated into South America during the formation of the Panamanian land bridge 3–5 million years ago. Patterns of population genetic divergence of each species were studied by phylogenetic analyses of mitochondrial DNA (mtDNA) control region sequences in individuals sampled across the distribution of these taxa. Abundant genetic diversity and remarkably concordant phylogeographic partitions for both species were observed, identifying parallel geographic regions which likely reflect historical faunal barriers. Inferred aspects of phylogeography, population genetic structure, and demographic history were used to formulate conservation recommendations for these species. In addition, observed patterns of sequence variation provided insight into the molecular evolution of the mtDNA control region in closely related felids. Received: 26 January 1998 / Accepted: 14 May 1998     

Genetic variation and island biogreography: Microsatellite and mitochondrial DNA variation in island populations of the Australian bush rat, Rattus fuscipes greyii

To understand the impact of various factors on the maintenance of genetic variation in natural populations, we need to focus on situations where at least some of these factors are removed or controlled. In this study, we used highly variable, presumably neutral, microsatellite and mtDNA markers to assess the nature of genetic variation in 14 island and two mainland populations of the Australian bush rat, where there is no migration between islands. Thus we are controlling for selection and gene flow. Both marker sets revealed low levels of diversity within the small island populations and extreme differentiation between populations. For six microsatellite loci, all of the small island populations had less genetic variation than the mainland populations; reduction in allelic diversity was more pronounced than loss of heterozygosity. Kangaroo Island, the large island population, had similar levels of diversity to the mainland populations. A 442 base pair (bp) section of the mtDNA control region was screened for variation by outgroup heteroduplex analysis/temperature gradient gel electrophoresis (OHA/TGGE). Only three of the 13 small island populations showed haplotypic diversity: Gambier (2), Waldegrave (2), and Eyere (3). The level of haplotypic diversity in the small island populations was similar to that on the mainland, most likely reflecting a recent population bottleneck on the mainland. In contrast, Kangaroo Island had 9 mtDNA haplotypes. The dominant factor influencing genetic diversity on the islands was island size. No correlation was detected between genetic diversity and the time since isolation or distance form the mainland. The combination of genetic drift within and complete isolation among the small island populations has resulted in rapid and extreme population divergence. Population pair-wise comparisons of allele frequency distributions showed significant differences for all populations for all loci (F _st = 0.11–0.84, R _st = 0.07–0.99). For the mtDNA control region, 92.6% of variation was apportioned between populations; only the Pearson islands shared a haplotype. Mantel tests of pair-wise genetic distance with pair-wise geographic distance showed no significant geographical clustering of haplotypes. However, population substructuring was detected within populations where sampling was conducted over a broader geographical range, as indicated by departures from Hardy-Weinberg equilibrium. Thus substructuring in the ancestral population cannot be ruled out. The dominant evolutionary forces on the islands, after the initial founder event, are stochastic population processes such as genetic drift and mutation. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular phylogeny of an endemic radiation of Cuban toads (Bufonidae: Peltophryne) based on mitochondrial and nuclear genes

Aim In this study we present a molecular phylogenetic and phylogeographical analysis of Peltophryne (Anura: Bufonidae), an endemic genus of Antillean toads, to investigate the spatial and temporal origins of the genus, with particular focus on the eight Cuban species. Location Greater Antilles, with extensive sampling of the Cuban archipelago. Methods We obtained DNA sequence data from two mitochondrial genes, cytochrome c oxidase subunit I (COI) and ribosomal RNA (16S), for 124 toads representing all eight Cuban species, and combined this with published data from Hispaniola (one of three species) and Puerto Rico (one of one species) to establish a molecular phylogeny for Peltophryne. In addition, we explored the phylogeographical structure of widespread Cuban species. For a subset of 42 toads we also obtained DNA sequence data from two nuclear genes, recombination activator‐1 (RAG‐1) and chemokine receptor 4 (CXCR‐4). We combined our molecular data with published DNA sequences from a global sample of bufonid toads to place the spatial and temporal origins of Peltophryne in the Caribbean within a fuller geographical and phylogenetic context. Results All phylogenetic analyses supported the monophyly of West Indian toads. The ancestor of Peltophyrne diverged from its mainland source around the Eocene–Oligocene boundary, with a subsequent radiation across the Caribbean islands taking place during the Miocene. Cuban species are monophyletic with a basal split in the early–middle Miocene that separates extant small‐bodied from large‐bodied species. Extensive mitochondrial DNA (mtDNA) sampling within widespread Cuban species revealed contrasting phylogeographical patterns. Peltophryne taladai and P. empusa showed deeply divergent lineages, whereas no geographical structure was observed in the widespread P. peltocephala. Main conclusions Our timeline for Peltophryne diversification is consistent with a biogeographical model requiring no long‐distance overwater dispersal. Although confidence intervals on divergence time estimates are wide, the stem age of Peltophyrne coincides with the hypothesized GAARlandia landspan or archipelago, which may have connected South America briefly with the Antilles. The ages of Peltophryne for Puerto Rico, Hispaniola and Cuba are consistent with a recently proposed vicariance scenario for the region. Our molecular results support the recognition of all eight species in Cuba, and provide evidence of possible cryptic species.     

Review of Antillean Glyptolenus Bates (Coleoptera: Carabidae), with description of a new species precinctive to St. Vincent

The Neotropical genus Glyptolenus Bates is represented in the West Indies by five species, three of which are geographically restricted to single islands; G. latelytra (Darlington) in Jamaica, G. simplicicollis Darlington in Dominica, and G. smithi, new species from St. Vincent. Glyptolenus chalybaeus (Dejean), widespread on the eastern South American mainland, extends northward through the Lesser Antilles to Montserrat. The fifth species, G. negrei Perrault, also widespread on the northern rim of South America, ranges only as far north as the continental island of Trinidad. The first four taxa have most likely achieved their distributions by over‐water dispersal from mainland South and Central America, possibly as many as four separate times. Their absence from the Greater Antilles of Cuba and Hispaniola is contrasted to the occurrence of multiple lineages on those islands in the closely related genus Platynus Bonelli.