DNA barcoding has revealed unrecognized species in several animal groups. In this study we have employed DNA barcoding to examine Hyalella, a taxonomically difficult genus of amphipod crustaceans, ...from sites in the southern Great Basin of California and Nevada, USA. We assessed the extent of species diversity using a species screening threshold (SST) set at 10 times the average intrapopulation cytochrome c oxidase subunit I (COI) haplotype divergence. Despite the fact that this threshold approach is more conservative in delineating provisional species than the phylogenetic species concept, our analyses revealed extraordinary levels of cryptic diversity and endemism. The SST discriminated two provisional species within Hyalella sandra, and 33 provisional species within Hyalella azteca. COI nucleotide divergences among these provisional species ranged from 4.4% to 29.9%. These results have important implications for the conservation of life in desert springs -- habitats that are threatened as a result of groundwater over-exploitation.
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•The Hyalella amphipod species cloud of ancient Lake Titicaca is polyphyletic.•Lake Titicaca was colonized at least 5 times independently.•Evolutionary radiation occurred within Lake ...Titicaca in two primarily endemic clades.•The dispersal history is complex, including migrations out of the lake.
Ancient lakes are renowned for their exceptional diversity of endemic species. As model systems for the study of sympatric speciation, it is necessary to understand whether a given hypothesized species flock is of monophyletic or polyphyletic origin. Here, we present the first molecular characterization of the Hyalella (Crustacea: Amphipoda) species complex of Lake Titicaca, using COI and 28S DNA sequences, including samples from the connected Small and Large Lakes that comprise Lake Titicaca as well as from a broader survey of southern South American sites. At least five evolutionarily distant lineages are present within Lake Titicaca, which were estimated to have diverged from one another 12–20 MYA. These major lineages are dispersed throughout the broader South American Hyalella phylogeny, with each lineage representing at least one independent colonization of the lake. Moreover, complex genetic relationships are revealed between Lake Titicaca individuals and those from surrounding water bodies, which may be explained by repeated dispersal into and out of the lake, combined with parallel intralacustrine diversification within two separate clades. Although further work in deeper waters will be required to determine the number of species present and modes of diversification, our results strongly indicate that this amphipod species cloud is polyphyletic with a complex geographic history.
Molecular studies have enlightened our understanding of freshwater zooplankton biogeography, yet questions remain regarding the scale and commonality of geographic speciation. Here, we present a ...mtDNA-based phylogenetic hypothesis for 92
Daphnia species from all seven continents, with a focus on North and South America, Europe, and Australia, and use it to explore the frequency, scale, and geographical orientation of allopatric divergence events. Allopatric speciation can conservatively account for at least 42% of cladogenetic events among the species included in our study; most of these involve intercontinental splits. Closely related species pairs are concentrated in the circumarctic region and between northern and southern continents, aligned with bird migration routes, suggesting recent dispersal. By contrast, deeper phylogenetic patterns are consistent with vicariance scenarios linked to continental fragmentation. The possible reasons for the puzzling persistence of these ancient patterns in light of the eroding force of dispersal are considered. Our results demonstrate the high frequency and complex pattern of allopatric speciation in this ancient, passively dispersed genus.
In this study we investigate the extent to which successive range fragmentations, postglacial expansions, and recolonizations influenced intraspecific genetic diversity and patterns of ...diversification in freshwater zooplankton. Specifically, we explore the global phylogeography of the Holarctic predatory cladoceran Leptodora kindtii Focke, 1844. Phylogenetic analyses based on the mitochondrial cytochrome c oxidase subunit I recover seven deeply divergent lineages (11.8–20.0%) comprising two sister clades within the Nearctic and east Palearctic and three related clades within the west Palearctic. Strong continental endemism was also supported by the nuclear 18S ribosomal gene. Intra-continental divergence levels (< 6%) suggest that many speciation events in Leptodora were initiated by glacial isolation. Demographic and network analyses indicate that in the Nearctic and west Palearctic, regions heavily affected by the Pleistocene glaciations, Leptodora persisted in both classic (e.g., Cascadia, Mississippi, southern Europe) and cryptic refugia (e.g., northeastern Europe, Carpathian basin). Strong signatures of late Pleistocene range expansions and secondary contact were observed in most clades. Deeper intraspecific phylogeographic structure occurs across much finer geographic scales in unglaciated regions of the east Palearctic than across glaciated Nearctic and west Palearctic regions. Leptodora’s ecological and biological characteristics, such as a reliance on temperate, permanent lakes, weak dispersal ability, and specific geological settings likely shaped the complex pattern of diversification in this important planktonic predator. Our data suggest the Pleistocene glaciations were important in the diversification of Holarctic freshwater zooplankton.
Aim To investigate the degree of phylogeographical divergence within pygmy whitefish (Prosopium coulterii) and to test hypotheses concerning the origin of disjunct populations within North America. ...Location North America from western Alaska to Lake Superior. Methods Mitochondrial (ATPase subunit VI) and nuclear (ITS-1, ITS-2) DNA sequence variation was assessed across the species' North American range to test for the existence of distinct phylogeographical groupings of pygmy whitefish associated with known glacial refugia. Coalescent simulations of the mitochondrial DNA (mtDNA) data were used to test hypotheses of population structure. Results This species is composed of two monophyletic mitochondrial clades across its North American range. The two mtDNA clades differed by an average 3.3% nucleotide sequence divergence. These clades were also distinguished by ITS-2, but the relationships among lineages were not resolved by the ITS-1 analysis. Coalescent analyses rejected the null hypothesis of the current disjunct distributions being a result of fragmentation of a single widespread ancestral lineage across a variety of effective population sizes and divergence times. Main conclusions The current range disjunctions of pygmy whitefish in North America probably resulted from isolation, genetic divergence, and selective dispersal from at least two major Pleistocene glacial refugia: Beringia and Cascadia. More recent isolation and dispersal from an upper Mississippi refugium is suggested by relationships within one of the clades and by distributional evidence from co-distributed species. The Beringian and Cascadian refugia have played major roles in the zoogeography of Nearctic temperate aquatics, but the roles of smaller refugia appear more variable among other species.
The copepod family Centropagidae is widely distributed and occurs in marine, estuarine, freshwater, and inland saline settings. Molecular phylogenies based upon the 16S and 28S genes demonstrate a ...complex biogeographic history, involving at least five independent invasions of continental waters from the sea. The first colonization was ancient, likely into part of Gondwanaland, and resulted in an inland radiation in southern genera via both vicariance and subsequent habitat shifting among different types of continental waters. Species occupying saline lakes are nested within freshwater clades, indicating invasion of these habitats via fresh waters rather than directly from the ocean or from epicontinental seas. In contrast with the great southern clade, all of the remaining continental invasions are northern, species poor, and quite recent, perhaps even Pleistocene. Long-lived evolutionary euryhalinity, a high propensity for inland invasion, continental vicariance, and
in situ radiation within single continents have all played major roles in the diversification of the centropagids.
The several thousand-fold range in genome size among animals has remained a subject of active research and debate for more than half a century, but no satisfactory explanation has yet been provided. ...Many one-dimensional models have been postulated, but so far none has been successful in accounting for observed patterns in genome size diversity. The recent model based on differences in effective population size appeared to gain empirical support with a study of genome size and inferred effective population size in fishes, but there were several questionable aspects of the analysis. First, it was based on an assumption that microsatellite heterozygosity indicates long-term effective population size, whereas in actuality these markers evolve quickly and are sensitive to demographic events. Second, it included both ancient polyploids and non-polyploids, the former of which did not gain their current genome sizes through the accumulation of slightly deleterious mutations as required in the model. Third, the analysis neglected the tremendous influence that Pleistocene glaciation bottlenecks had on heterozygosities in freshwater (and far less so, marine) fishes. In sum, it is apparent that genomes reached their current sizes in most fishes long before contemporary microsatellite heterozygosities were shaped, and that ancient polyploidy rather than the accumulation of mildly deleterious transposon insertions in small populations is the dominant factor that has influenced the large end of the range of genome sizes among fishes.
The predatory cladoceran Cercopagis pengoi has extended its range over the past decade from the Ponto-Caspian basin into the Baltic Sea and the Laurentian Great Lakes. This study employs ...mitochondrial DNA (mtDNA) sequence analysis to elucidate the invasion corridors exploited during this range expansion. The Caspian and Black Sea populations of C. pengoi exhibit marked genetic divergence, enabling their discrimination as potential sources of the Baltic and Great Lakes populations. The limited mtDNA haplotype diversity detected in the Baltic populations suggests they were founded by a small number of colonists from the Black Sea. The colonization of North America was apparently a result of the transfer of animals from the Baltic Sea in ballast water.
Daphnia ambigua, one of the most broadly distributed members of its genus, occurs in Europe as well as in North and South America. This investigation examines diversity in two mitochondrial genes, ...COI and 12S rDNA, to ascertain the geographical distribution of variation in this species. The results establish that North American D. ambigua are separable into four phylogroups with an average of 4% mtDNA sequence divergence. One of these groups is dominant, occupying Mexico and the central United States, whereas the other groups are restricted to the Atlantic or Pacific coasts. Their distributional centroids coincide with refugial areas identified in prior studies, reinforcing evidence that the Appalachian and West Coast ranges have been important in the isolation of zooplankton lineages. Gene exchange, mediated by migratory birds whose flyways are structured by these mountains, is likely instrumental in maintaining north-south cohesion within each phylogroup. European populations of D. ambigua are closely allied to those from the eastern United States, a result concordant with their presumed recent introduction from North America. By contrast, South American populations last shared an ancestor with North American lineages approximately 2 million yr ago. The phylogeographic information now available suggests that topographic barriers generate predictable patterns of population divergence in zooplankton species and that allopatric speciation has played an important role in their diversification.
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