Phylogeography of a widespread Australian freshwater fish, western carp gudgeon (Eleotridae: Hypseleotris klunzingeri): Cryptic species, hybrid zones, and strong intra-specific divergences.

Despite belonging to the most abundant and widespread genus of freshwater fishes in the region, the carp gudgeons of eastern Australia (genus Hypseleotris) have proved taxonomically and ecologically problematic to science since the 19th century. Several molecular studies and a recent taxonomic revision have now shed light on the complex biology and evolutionary history that underlies this group. These studies have demonstrated that carp gudgeons include a sexual/unisexual complex (five sexual species plus an assortment of hemiclonal lineages), many members of which also co-occur with an independent sexual relative, the western carp gudgeon (H. klunzingeri). Here, we fill yet another knowledge gap for this important group by presenting a detailed molecular phylogeographic assessment of the western carp gudgeon across its entire and extensive geographic range. We use a suite of nuclear genetic markers (SNPs and allozymes) plus a matrilineal genealogy (cytb) to demonstrate that H. klunzingeri s.l. also displays considerable taxonomic and phylogeographic complexity. All molecular datasets concur in recognizing the presence of multiple candidate species, two instances of historic between-species admixture, and the existence of a natural hybrid zone between two of the three candidate species found in the Murray-Darling Basin. We also discuss the major phylogeographic patterns evident within each taxon. Together, these analyses provide a robust molecular, taxonomic, and distributional framework to underpin future morphological and ecological investigations on this prominent member of regional freshwater ecosystems in eastern Australia.

Molecular evidence for sequential colonization and taxon cycling in freshwater decapod shrimps on a Caribbean island.

Taxon cycling, i.e. sequential phases of expansions and contractions in species' distributions associated with ecological or morphological shifts, are postulated to characterize dynamic biogeographic histories in various island faunas. The Caribbean freshwater shrimp assemblage is mostly widespread and sympatric throughout the region, although one species (Atyidae: Atya lanipes) is geographically restricted and ecologically and morphologically differentiated from other Atya species. Using patterns of nucleotide variation at the COI mtDNA gene in five species of freshwater shrimp (A. lanipes, A. scabra, A. innocuous; Xiphocarididae: Xiphocaris elongata; Palaemonidae: Macrobrachium faustinum) from Puerto Rico, we expected to detect a signature of sequential colonization in these shrimp, consistent with the concept of taxon cycling, and expected that A. lanipes would be at a different taxon stage (i.e. an early stage species) to all other species. We also examined patterns of genetic population structure in each species expected with poor, intermediate and well-developed abilities for among-river dispersal. Population expansions were detected in all species, although the relative timing of the expansions varied among them. Assuming that population expansions followed colonization of Puerto Rico by freshwater shrimp, results bear the hallmarks of sequential colonization and taxon cycling in this fauna. A. lanipes had a star phylogeny, low mean pairwise nucleotide differences and recent (Holocene) estimates for an in situ population expansion in Puerto Rico, and it was inferred as an early stage species in the taxon cycle undergoing a secondary phase of expansion. All other species were inferred as late stage species undergoing regional population expansions, as their mean pairwise nucleotide differences were relatively high and phylogenetic patterns were more complex than A. lanipes. High rates of gene flow without isolation by distance among rivers were detected in all species, although results should be treated cautiously as some populations are unlikely to be in mutation-drift equilibrium. Nested clade analysis produced inconsistent results among species that all have high rates of gene flow and expanding populations.

Phylogeography of an Island endemic, the Puerto Rican Freshwater Crab (Epilobocera sinuatifrons).

The endemic Puerto Rican crab, Epilobocera sinuatifrons (Pseudothelphusidae), has a freshwater-dependant life-history strategy, although the species has some capabilities for terrestrial movement as adults. In contrast to all other freshwater decapods on the island (e.g., caridean shrimp), E. sinuatifrons does not undertake amphidromous migration, and is restricted to purely freshwater habitats and adjacent riparian zones. As Puerto Rico has a dynamic geologic history, we predicted that both the life history of E. sinuatifrons and the geological history of the island would be important determinants of phylogeographic structuring in the species. Using a fragment of the cytochrome c oxidase subunit 1 mtDNA (mitochondrial DNA) gene, we tested for deviations from panmixia among and within rivers draining Puerto Rico and used statistical phylogeography to explore processes that may explain extant patterns of genetic variation in the species. While populations of E. sinuatifrons were significantly differentiated among rivers, they were likely to be recently derived because nested clade analysis (NCA) indicated evolutionarily recent restricted gene flow with isolation by distance (IBD) and contiguous range expansion at various spatial scales. Ongoing drainage rearrangements associated with faulting and land slippage were invoked as processes involved in sporadic gene flow among rivers throughout the Pleistocene. Patterns of genetic differentiation conformed to IBD and population demographic statistics were nonsignificant, indicating that although recently derived, populations from different rivers were in drift-mutation equilibrium. A shallow (0.6 million years ago), paraphyletic split was observed in the haplotype network, which NCA indicated arose via allopatric fragmentation. This split coincides with an area of high relief in central Puerto Rico that may have experienced relatively little drainage rearrangements. Shallow but significant genetic isolation of populations of E. sinuatifrons among Puerto Rican rivers suggests phylogeographic patterns that are intermediate to terrestrial habitat specialists (highly divergent populations) and other freshwater biota, such as amphidromous species and insects with aerial adult dispersal (highly connected populations).