Two deep evolutionary lineages in the circumtropical glasseye Heteropriacanthus cruentatus (Teleostei,Priacanthidae) with admixture in the south‐western Indian Ocean

A phylogeographic study of the circumtropical glasseye Heteropriacanthus cruentatus was conducted. Molecular analyses indicate two mitochondrial cytochrome c oxidase subunit I (coI) lineages that are 10·4% divergent: one in the western Atlantic (Caribbean) and another that was detected across the Indo‐Pacific. A fixed single nucleotide polymorphism (SNP) was detected at a nuclear locus (S7 ribosomal protein) and is consistent with this finding. There is evidence of recent dispersal from the Atlantic to the Indian Ocean with individuals of mixed lineages detected in South Africa and the Mozambique Channel. Using coalescent analyses of the mitochondrial dataset, time of divergence between lineages was estimated to be c. 15·3 million years. The deep divergence between these two lineages indicates distinct evolutionary units, however, due to the lack of morphological differences and evidence of hybridization between lineages, taxonomic revision is not suggested at this time.     

EVIDENCE OF A BIOGEOGRAPHIC BREAK BETWEEN POPULATIONS OF A HIGH DISPERSAL STARFISH: CONGRUENT REGIONS WITHIN THE INDO-WEST PACIFIC DEFINED BY COLOR MORPHS,mtDNA, AND ALLOZYME DATA

Both mtDNA variation and allozyme data demonstrate that geographic groupings of different color morphs of the starfish Linckia laevigata are congruent with a genetic discontinuity between the Indian and Pacific Oceans. Populations of L. laevigata sampled from Thailand and South Africa, where an orange color morph predominates, were surveyed using seven polymorphic enzyme loci and restriction fragment analysis of a portion of the mtDNA including the control region. Both allozyme and DNA data demonstrated that these populations were significantly genetically differentiated from each other and to a greater degree from 23 populations throughout the West Pacific Ocean, where a blue color morph is predominant. The genetic structure observed in L. laevigata is consistent with traditional ideas of a biogeographic boundary between the Indian and Pacific Oceans except that populations several hundreds kilometers off the coast of north Western Australia (Indian Ocean) were genetically similar to and had the same color morphs as Pacific populations. It is suggested that gene flow may have continued (possibly at a reduced rate) between these offshore reefs in Western Australia and the West Pacific during Pleistocene falls in sea level, but at the same time gene flow was restricted between these Western Australian populations and those in both Thailand and South Africa, possibly by upwellings. The molecular data in this study suggest that vicariant events have played an important role in shaping the broadscale genetic structure of L. laevigata. Additionally, greater genetic structure was observed among Indian Ocean populations than among Pacific Ocean populations, probably because there are fewer reefs and island archipelagos in the Indian Ocean than in the Pacific, and because present-day surface ocean currents do not facilitate long-distance dispersal.     

POSTZYGOTIC GENETIC INCOMPATIBILITY BETWEEN SYMPATRIC COLOR MORPHS

Alternative genetically determined color morphs within a population or species are believed to successfully interbreed within a population. However, the occurrence of prezygotic or ecological selection in a number of polymorphic systems may lead to nonrandom mating and prevent genetic morphs from fully interbreeding. Here we show that postzygotic incompatibility significantly limits gene flow between the sympatric red and black color morphs of the Gouldian finch ( Erythrura gouldiae ). Using a balanced within-female experimental design, in which individuals were forced to breed in pure and mixed morph crosses, we found large inviability effects (>30%) in offspring resulting from genetically mixed genotypes. The consistent mortality effects across different stages of development (e.g., prehatching, juvenile, adulthood), unconfounded by environmentally derived parental effects or social environments, reveal an underlying genetic incompatibility between different genotypes. Furthermore, mortality in mixed morph genotypes was particularly severe (43.6%) for the heterogametic sex (daughters), which is consistent with Haldane's rule predicted for postzygotic incompatibilities between hybridizing species. This significant, but incomplete, postzygotic isolation suggests that the sympatric morphs may represent transient stages in the speciation–hybridization process.     

EVOLUTION OF ASEXUALITY IN THE COSMOPOLITAN MARINE CLAM LASAEA

The marine clam genus Lasaea is unique among marine bivalves in that it contains both sexual and asexual lineages. We employed molecular tools to infer intrageneric relationships of geographically restricted sexual versus cosmopolitan asexual forms. Polymerase chain reaction primers were used to amplify and sequence homologous 624 nucleotide fragments of COIII from polyploid, asexual, direct-developing individuals representing northeastern Pacific, northeastern Atlantic, Mediterranean, southern Indian Ocean, and Australian populations. DNA sequences also were obtained from the two known diploid congeners, the Australian sexual, indirect developer, Lasaea australis, and an undescribed meiotic Australian direct developer. Estimated tree topologies did not support monophyly for polyploid asexual Lasaea lineages. A robust dichotomy was evident in all phylogenetic trees and each of the two main branches included one of the diploid meitoic Australian congeners. Lasaea australis clustered with two of the direct-developing, polyploid asexual haplotypes, one from Australia, the other from the northeastern Atlantic. Monophyly is supported for the diploid Australian direct-developing lineage together with the remaining polyploid asexual lineages from the northeastern Pacific, northeastern Atlantic, Mediterranean, and southern Indian Ocean. These results indicate that asexual Lasaea lineages are polyphyletic and may have resulted from multiple hybridization events. The high degree of genetic divergence of asexual lineages from co-clustering meiotic congeners (16%–22%) and among geographically restricted monophyletic clones (9%–11%) suggests that asexual Lasaea lineages may be exceptionally long lived.     

Introgressive hybridization between color morphs in a population of cichlid fishes twelve years after human-induced secondary admixis

In the extremely species-rich haplochromine cichlid fishes of the East African Great Lakes, prezygotic isolation between closely related species is often maintained by color-assortative mating. In 1998, local fisherman working for the ornamental fish trade released different color morphs of the cichlid genus Tropheus into a small harbor basin in the southern part of Lake Tanganyika. This artificial amalgamation of color morphs provides a unique possibility to study mating patterns in cichlids in a natural environment over time. In a precursor study, we analyzed genotypes and phenotypes of almost 500 individuals sampled between 1999 and 2001 and uncovered a marked degree of color-assortative mating, which depended on the level of color pattern dissimilarity between morphs. Twelve years after introduction of nonindigenous morphs, we again sampled Tropheus individuals from the harbor basin and an adjacent, originally pure population and analyzed phenotypes (coloration) and genotypes (mitochondrial control region and 9 microsatellite loci) to assess the current status of the admixed population. Principal component analyses of color score data and population assignment tests demonstrate an increasing level of introgressive hybridization between morphs but also some ongoing color-assortative mating within morphs. The observed mating pattern might have been influenced by fluctuating environmental conditions such as periodic algal blooms or increased sedimentation causing turbid conditions in an otherwise clear lake.     

Opening a can of worms: unprecedented sympatric cryptic diversity within British lumbricid earthworms

Earthworms play a major role in many aspects of soil fertility, food web ecology and ecosystem functioning, and hence are frequently the subjects of, for example, ecological and toxicological research. Our aim was to examine the genetic structure of common earthworm species, to identify cryptic lineages or species that may be distinct ecotypes or biotypes (and hence confound current research based upon morphotypes) and to try to explain the massive cryptic diversity that eventually emerged. We demonstrated that species such as Allolobophora chlorotica, Aporrectodea longa, Aporrectodea rosea and Lumbricus rubellus all comprise highly divergent lineages with species-level divergence at the mitochondrial cytochrome oxidase I (COI) gene. In Allo. chlorotica alone, we found 55 haplotypes for COI, with 35 of these being found in pink and 20 in green morph worms. There were no cases of the two colour morphs sharing COI haplotypes. Phylogenetic analyses of mitochondrial COI and 16S genes showed the presence of five highly divergent lineages, suggesting the presence of multiple cryptic species within Allo. chlorotica. There was no clear geographical pattern to lineage distribution and many populations were polymorphic for both mitochondrial DNA lineage and colour morph. Amplified fragment length polymorphism results, based on two primer combinations, were broadly congruent with mitochondrial DNA results with one significant exception. Despite showing over 14% divergence at COI, amplified fragment length polymorphism markers showed that the two green morph lineages may be interbreeding and therefore represent a single taxon. The cryptic diversity revealed by these results has profound consequences for all areas of earthworm research.     

The Isthmus of Panama: a major physical barrier to gene flow in a highly mobile pantropical seabird

To further test the hypothesis that the Isthmus of Panama is a major barrier to gene flow in pantropical seabirds, we applied phylogeographic methods to mitochondrial control sequence variation in masked booby (Sula dactylatra) populations on either side of the Isthmus of Panama and the southern tip of Africa. In accord with Steeves et al. (2003), we found that all Caribbean masked boobies with the 'secondary contact' cytochrome b haplotype (m-B) shared a control region haplotype (Sd_100), which grouped with Indian-Pacific haplotypes and not Caribbean-Atlantic haplotypes. In addition, Sd_100 was more closely related to control region haplotypes in the Indian Ocean than in the Pacific. We also found that the 'secondary contact' birds diverged more recently from extant populations in the Indian Ocean than in the Pacific. Thus, it appears that these masked boobies did not breach the Isthmus of Panama. Rather, birds likely dispersed around the southern tip of Africa during favourable oceanographic conditions in the Pleistocene.     

Geographic Patterns of Genetic Variation in a Broadly Distributed Marine Vertebrate: New Insights into Loggerhead Turtle Stock Structure from Expanded Mitochondrial DNA Sequences

Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (∼800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting comprehensive international cooperative data management and research in marine ecology.     

Ubiquity of Sicyopterus lagocephalus (Teleostei: Gobioidei) and phylogeography of the genus Sicyopterus in the Indo-Pacific area inferred from mitochondrial cytochrome b gene

Sicyopterus lagocephalus is a Gobiidae Sicydiinae (Teleostei) thought to inhabit Indo-Pacific island rivers from Comoros Islands in the Indian Ocean to Australs Islands (French Polynesia) in the Pacific Ocean. Its biological cycle comprises a marine planctonic larval phase of several months allowing it to migrate from island to island, but the other species of the genus, with such a larval stage, have generally a more restricted range and are often endemic. To understand the organisation of a species with such a wide distribution, mtDNA cytochrome b sequences were amplified for 55 specimens of this genus covering most of its distribution range together with six close endemic species and other gobiids used as outgroups. The main result is the confirmation of the ubiquity of S. lagocephalus that occurs over a range of 18,000 km in the Indian and Pacific Oceans. Two clades were identified within this species, one clustering most of French Polynesian haplotypes and the other clustering most of Mascarene (including Comoros) haplotypes. The overall pattern of distribution and phylogenetic relationship suggests that the lineages leading to endemic species originated earlier than S. lagocephalus. This latter seems to be a secondary migrant species, having colonised both Indian and Pacific Oceans with a few exceptions, situated at the border of the range (Madagascar, Marquesas, Rapa). According to the results, the phylogeny of the Sicyopterus group, the age of the different lineages and the past history of the colonisation of the Indo-Pacific islands are discussed.     

Global distribution of cryptic native,introduced and hybrid lineages in the widespread estuarine amphipod Ampithoe valida

Biological invasions can pose a severe threat to coastal ecosystems, but are difficult to track due to inaccurate species identifications and cryptic diversity. Here, we clarified the cryptic diversity and introduction history of the marine amphipod Ampithoe valida by sequencing a mtDNA locus from 683 individuals and genotyping 10,295 single-nucleotide polymorphisms (SNPs) for 349 individuals from Japan, North America and Argentina. The species complex consists of three cryptic lineages: two native Pacific and one native Atlantic mitochondrial lineage. It is likely that the complex originated in the North Pacific and dispersed to the north Atlantic via a trans-arctic exchange approximately 3 MYA. Non-native A. valida in Argentina have both Atlantic mitochondrial and nuclear genotypes, strongly indicating an introduction from eastern North America. In two eastern Pacific estuaries, San Francisco Bay and Humboldt Bay, California, genetic data indicate human-mediated hybridization of Atlantic and Pacific sources, and possible adaptive introgression of mitochondrial loci, nuclear loci, or both. The San Francisco Bay hybrid population periodically undergoes population outbreaks and profoundly damages eelgrass Zostera marina thalli via direct consumption, and these ecological impacts have not been documented elsewhere. We speculate that novel combinations of Atlantic and Pacific lineages could play a role in A. valida’s unique ecology in San Francisco Bay. Our results reinforce the notion that we can over-estimate the number of non-native invasions when there is cryptic native structure. Moreover, inference of demographic and evolutionary history from mitochondrial loci may be misleading without simultaneous survey of the nuclear genome.

     

Hybrid zone structure and the potential role of selection in hybridizing populations of native westslope cutthroat trout (Oncorhynchus clarki lewisi) and introduced rainbow trout (O. mykiss)

Introgressive hybridization is a common feature of many zones of contact between divergent lineages of fishes. This is particularly common when taxa that are normally allopatric come into artificial (human-induced) secondary contact. We examined 18 native populations of westslope cutthroat trout (Oncorhynchus clarki lewisi, WCT) to determine the extent of introgressive hybridization with introduced rainbow trout (O. mykiss, RBT) and the genetic structure of hybridizing populations in the upper Kootenay River, southeastern British Columbia, Canada. Using four diagnostic nuclear loci we calculated a hybrid index, inbreeding coefficient, FIS, and the linkage disquilibrium correlation coefficient, Rij, for each locality to determine the distribution of genotypes in each population. We also categorized the 142 hybrid individuals found across localities into four hybrid classes based on their genotypes. The majority of localities (11/18) showed a unimodal distribution of genotypes skewed towards genotypes of WCT. Two localities, however (lower Gold Creek and Lodgepole Creek) showed a flat to bimodal distribution and one site (lower Bull River) showed a unimodal distribution skewed towards RBT genotypes. The majority of hybrid individuals were classified genotypically as WCT backcrosses (59%) and post-F1 individuals (24%). We found a skewed ratio of pure WCT to pure RBT (17:1) and only four F1 hybrids (3%), suggesting that the spread of RBT alleles may be facilitated by hybrids straying to neighbouring populations. We also tested for the action of selection in one population using cohort analyses, but found little evidence of differential selection between pure WCT and hybrid individuals. Pooled across age classes there were significant differences in genotypic frequencies among loci suggesting differential introgression. There was no asymmetry to the hybridization between rainbow trout and westslope cutthroat trout because both species' mitochondrial DNA haplotypes were observed at similar frequencies in the hybrids. Our analyses suggest that hybrid swarms are likely to form in the upper Kootenay River drainage and that certain native WCT populations in British Columbia are at risk of local genomic extinction.     

Multiple population structure of the giant mottled eel, Anguilla marmorata

The population structure of the giant mottled eel, Anguilla marmorata, was investigated with mitochondrial and microsatellite DNA analyses using 449 specimens from 13 localities throughout the species range. Control region F-statistics indicated the North Pacific (Japan, Taiwan, Philippines, Sulawesi), South Pacific (Tahiti, Fiji, New Caledonia, Papua New Guinea), eastern Indian Ocean (Sumatra), western Indian Ocean (Réunion, Madagascar), Ambon, and Guam regions were significantly different (Phi(ST) = 0.131-0.698, P < 0.05) while only a few differences were observed between localities within the South Pacific. These regions were roughly clustered in the neighbour-joining tree, although Ambon individuals were mainly divided into North and South Pacific groups. Analysis with eight microsatellite loci showed almost identical results to those of the control region, except no genetic difference was observed between the western and eastern Indian Ocean (F(ST) = 0.009, P > 0.05). The Bayesian cluster analysis of the microsatellite data detected two genetic groups. One included four North Pacific localities, and the other included eight localities in the South Pacific, Indian Ocean, and Guam, but Ambon individuals were evenly assigned to these two groups. These results showed that A. marmorata has four genetically different populations (North Pacific, South Pacific, Indian Ocean, Guam region). The North Pacific population is fully panmictic whereas the South Pacific and Indian Ocean populations have a metapopulation structure. Interestingly, Guam was suggested to be inhabited by a reproductive population restricted to that region, and the individuals from the North and South Pacific populations co-exist in Ambon.     

A mitochondrial phylogeography of Brachidontes variabilis (Bivalvia: Mytilidae) reveals three cryptic species

This study examined genetic variation across the range of Brachidontes variabilis to produce a molecular phylogeography. Neighbour joining (NJ), minimum evolution (ME) and maximum parsimony (MP) trees based on partial mitochondrial DNA sequences of 16S-rDNA and cytochrome oxidase (COI) genes revealed three monophyletic clades: (1) Brachidontes pharaonis s.l. from the Mediterranean Sea and the Red Sea; (2) B. variabilis from the Indian Ocean; (3) B. variabilis from the western Pacific Ocean. Although the three clades have never been differentiated by malacologists employing conventional morphological keys, they should be ascribed to the taxonomic rank of species. The nucleotide divergences between Brachidontes lineages (between 10.3% and 23.2%) were substantially higher than the divergence between congeneric Mytilus species (2.3–6.7%) and corresponded to interspecific divergences found in other bivalvia, indicating that they should be considered three different species. Analysis of the 16S-rDNA sequences revealed heteroplasmy, indicating dual uniparental inheritance (DUI) of mtDNA in the species of Brachidontes collected in the Indian Ocean, but not in the species in the Pacific nor in the species in the Red Sea and the Mediterranean Sea. When we employed the conventional estimate of the rate of mitochondrial sequence divergence (2% per million years), the divergence times for the three monophyletic lineages were 6–11 Myr for the Indian Ocean and Pacific Ocean Brachidontes sp. and 6.5–9 Myr for the Red Sea and Indian Ocean Brachidontes sp . Thus, these species diverged from one another during the Miocene (23.8–5.3 Myr). We infer that a common ancestor of the three Brachidontes species probably had an Indo-Pacific distribution and that vicariance events, linked to Pleistocene glaciations first and then to the opening of the Red Sea, produced three monophyletic lineages.     

Worldwide phylogeography of the blacktip shark (Carcharhinus limbatus) inferred from mitochondrial DNA reveals isolation of western Atlantic populations coupled with recent Pacific dispersal

Although many coastal shark species have widespread distributions, the genetic relatedness of worldwide populations has been examined for few species. The blacktip shark, (Carcharhinus limbatus), inhabits tropical and subtropical coastal waters throughout the world. In this study, we examined the genetic relationships of blacktip shark populations (n = 364 sharks) throughout the majority of the species' range using the entire mitochondrial control region (1067-1070 nucleotides). Two geographically distinct maternal lineages (western Atlantic, Gulf of Mexico, and Caribbean Sea clades, and eastern Atlantic, Indian, and Pacific Ocean clades) were identified and shallow population structure was detected throughout their geographic ranges. These findings indicate that a major population subdivision exists across the Atlantic Ocean, but not the Pacific Ocean. The historical dispersal of this widespread, coastal species may have been interrupted by the rise of the Isthmus of Panama. This scenario implies historical dispersal across the Pacific Ocean (supported by the recovery of the same common haplotype from the Philippines, Hawaii, and the Gulf of California reflecting recent/contemporary dispersal abilities) and an oceanic barrier to recent migration across the Atlantic. Genetic structure within the eastern Atlantic/Indo-Pacific (Phi(ST) = 0.612, P < 0.001) supports maternal philopatry throughout this area, expanding previous western Atlantic findings. Eastern Atlantic/Indo-Pacific C. limbatus control region haplotypes were paraphyletic to Carcharhinus tilstoni haplotypes in our maximum-parsimony analysis. The greater divergence of western Atlantic C. limbatus than C. tilstoni from eastern Atlantic/Indo-Pacific C. limbatus reflects the taxonomic uncertainty of western Atlantic C. limbatus.     

Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population

Hybridization between divergent lineages generates new allelic combinations. One mechanism that can hinder the formation of hybrid populations is mitonuclear incompatibility, that is, dysfunctional interactions between proteins encoded in the nuclear and mitochondrial genomes (mitogenomes) of diverged lineages. Theoretically, selective pressure due to mitonuclear incompatibility can affect genotypes in a hybrid population in which nuclear genomes and mitogenomes from divergent lineages admix. To directly and thoroughly observe this key process, we de novo sequenced the 747‐Mb genome of the coastal goby, Chaenogobius annularis, and investigated its integrative genomic phylogeographics using RNA‐sequencing, RAD‐sequencing, genome resequencing, whole mitogenome sequencing, amplicon sequencing, and small RNA‐sequencing. Chaenogobius annularis populations have been geographically separated into Pacific Ocean (PO) and Sea of Japan (SJ) lineages by past isolation events around the Japanese archipelago. Despite the divergence history and potential mitonuclear incompatibility between these lineages, the mitogenomes of the PO and SJ lineages have coexisted for generations in a hybrid population on the Sanriku Coast. Our analyses revealed accumulation of nonsynonymous substitutions in the PO‐lineage mitogenomes, including two convergent substitutions, as well as signals of mitochondrial lineage‐specific selection on mitochondria‐related nuclear genes. Finally, our data implied that a microRNA gene was involved in resolving mitonuclear incompatibility. Our integrative genomic phylogeographic approach revealed that mitonuclear incompatibility can affect genome evolution in a natural hybrid population.     

Mito‐nuclear discordance at a mimicry color transition zone in bumble bee Bombus melanopygus

As hybrid zones exhibit selective patterns of gene flow between otherwise distinct lineages, they can be especially valuable for informing processes of microevolution and speciation. The bumble bee, Bombus melanopygus, displays two distinct color forms generated by Müllerian mimicry: a northern “Rocky Mountain''’ color form with ferruginous mid‐abdominal segments (B. m. melanopygus) and a southern “Pacific''’ form with black mid‐abdominal segments (B. m. edwardsii). These morphs meet in a mimetic transition zone in northern California and southern Oregon that is more narrow and transitions further west than comimetic bumble bee species. To understand the historical formation of this mimicry zone, we assessed color distribution data for B. melanopygus from the last 100 years. We then examined gene flow among the color forms in the transition zone by comparing sequences from mitochondrial COI barcode sequences, color‐controlling loci, and the rest of the nuclear genome. These data support two geographically distinct mitochondrial haplogroups aligned to the ancestrally ferruginous and black forms that meet within the color transition zone. This clustering is also supported by the nuclear genome, which, while showing strong admixture across individuals, distinguishes individuals most by their mitochondrial haplotype, followed by geography. These data suggest the two lineages most likely were historically isolated, acquired fixed color differences, and then came into secondary contact with ongoing gene flow. The transition zone, however, exhibits asymmetries: mitochondrial haplotypes transition further south than color pattern, and both transition over shorter distances in the south. This system thus demonstrates alternative patterns of gene flow that occur in contact zones, presenting another example of mito‐nuclear discordance. Discordant gene flow is inferred to most likely be driven by a combination of mimetic selection, dominance effects, and assortative mating.     

Resurrection of Indian Ocean humbug damselfish,Dascyllus abudafur (Forsskål) from synonymy with its Pacific Ocean sibling,Dascyllus aruanus (L.)

Previous phylogeographic studies of the humbug damselfish, a widespread Indo-West Pacific coral reef fish, have revealed a split of two main mitochondrial lineages distributed on either side of the Indo-Pacific barrier. This has been interpreted as the result of vicariance. It has been hypothesized that reproductive barriers might currently limit gene flow between humbug damselfish populations from the Indian Ocean and the Pacific Ocean. In this study, we review the published phylogeographic information to update the distribution of the two main mitochondrial lineages of humbug damselfish. The Indian lineage was distributed from the Red Sea to the eastern extremity of the Sunda Shelf while the Pacific lineage, which diverged from the former by 0.6% net nucleotide divergence and diagnostic substitutions at three nucleotide sites at the cytochrome b locus, was distributed east and north of the Sunda Shelf. The two forms, which are also genetically distinct at nuclear loci, were also characterized by distinct pigmentation patterns. We argue that the two forms represent geminate species. Epithet aruanus Linnaeus is maintained for the Pacific Ocean humbug damselfish while epithet abudafur (Forsskål) is here resurrected for the Indian Ocean humbug damselfish. Future studies should focus on the population genetic structure of the transition zone between Dascyllus abudafur and D. aruanus.     

Indo-Pacific population structure and evolutionary history of the coconut crab Birgus latro

Mitochondrial DNA variation was used to examine population structure in a widespread, marine-dispersed species, Birgus latro . Crabs were collected from eight locations throughout the species' Indo-Pacific distribution. Purified mtDNA from 160 individuals was cut with five restriction enzymes, revealing high haplotype diversity (0.96) and moderate nucleotide diversity (0.75%). Island populations from the Indian Ocean (Christmas I.) and Pacific Ocean were significantly different ( G _ST= 0.37) and had distinct mtDNA lineages with a net sequence divergence of 1.4%. Pacific island populations had diverged in a manner consistent with isolation by distance, with only the most peripheral populations being significantly different. The results for mtDNA are largely concordant with those from allozymes, although estimates of gene flow between the Indian and Pacific Oceans were much lower when based on mtDNA. The mtDNA phylogeny also permitted a deeper examination of the evolutionary and demographic history of Birgus latro . Long-term separation of populations is evident in the complete phylogenetic subdivision of mtDNA lineages between the Indian and Pacific Ocean populations sampled. The starlike phylogeny of alleles from the Pacific suggests a rapid population expansion in the Pacific during the Pleistocene. Including information about allele phylogeny, as well as distribution and frequency, obscured contemporary population structure, but provided unique insights into the evolutionary history of the species.     

Diagnostic SNPs reveal widespread introgressive hybridization between introduced bighead and silver carp in the Mississippi River Basin

Hybridization among conspecifics in native and introduced habitats has important implications for biological invasions in new ecosystems. Bighead (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are genetically isolated and occur in sympatry within their native range. Following their introduction to North America, however, introgressant hybrids have been reported throughout their expanded range within the Mississippi River Basin (MRB). The extent of introgression, both spatially and generationally, is largely unknown. Therefore, we examined mixed‐species populations from across the MRB to characterize the extent of interspecific gene flow. We assayed 2798 individuals from nine locations with a suite of species‐diagnostic SNPs (57 nuclear and one mitochondrial). Forty‐four per cent (n = 1244) of individuals displayed hybrid genotypes. Moreover, the composition of hybrid genotypes varied among locations and represented complex hybrid swarms with multiple generations of gene flow. Introgressive hybrids were identified from all locations, were bidirectional and followed a bimodal distribution consisting primarily of parental or parental‐like genotypes and phenotypes. All described hybrid categories were present among individuals from 1999 to 2008, with parents and later‐generation backcrosses representing the largest proportion of individuals among years. Our mitochondrial SNP (COII), tested on a subset of 730 individuals, revealed a silver carp maternal bias in 13 of 21 (62%) F₁ hybrids, in all silver carp backcrosses, and maintained throughout many of the bighead carp backcrosses. The application of this suite of diagnostic markers and the spatial coverage permits a deeper examination of the complexity in hybrid swarms between two invasive, introduced species.