Molecular phylogeny reveals extensive ancient and ongoing radiations in a snapping shrimp species complex (Crustacea, Alpheidae, Alpheus armillatus).

Tropical marine habitats often harbor high biodiversity, including many cryptic taxa. Though the prevalence of cryptic marine taxa is well known, the evolutionary histories of these groups remain poorly understood. The snapping shrimp genus Alpheus is a good model for such investigations, as cryptic species complexes are very common, indicating widespread genetic diversification with little or no morphological change. Here, we present an extensive phylogeographic investigation of the diversified amphi-American Alpheus armillatus species complex, with geographic sampling in the Caribbean Sea, Gulf of Mexico, Florida, Brazil, and the tropical Eastern Pacific. Sequence data from two mitochondrial genes (16SrRNA and cytochrome oxidase I) and one nuclear gene (myosin heavy chain) provide strong evidence for division of the species complex into six major clades, with extensive substructure within each clade. Our total data set suggests that the A. armillatus complex includes no less than 19 putative divergent lineages, 11 in the Western Atlantic and 8 in the Eastern Pacific. Estimates of divergence times from Bayesian analyses indicate that the radiation of the species complex began approximately 10 MYA with the most recent divergences among subclades dating to within the last 3 MY. Furthermore, individuals from the six major clades had broadly overlapping geographic distributions, which may reflect secondary contact among previously isolated lineages, and have apparently undergone several changes in superficial coloration, which is typically the most pronounced phenotypic character distinguishing lineages. In addition, the extensive substructure within clades indicates a great deal of molecular diversification following the rise of the Isthmus of Panama. In summary, this investigation reflects substantial biodiversity concealed by morphological similarity, and suggests that both ancient and ongoing divergences have contributed to the generation of this biodiversity. It also underlines the necessity to work with the most complete data set possible, which includes comprehensive and wide-ranging sampling of taxa.

Distance communication of sexual status in the crayfish Orconectes quinebaugensis: female sexual history mediates male and female behavior.

Chemical communication plays an important role in mediating social interactions of many taxa, particularly arthropods. Many individuals communicate information about their reproductive status to potential mates through distance and/or contact pheromones, an ability that may be advantageous to both signalers and receivers. In this paper, we describe tests of two hypotheses on the role of distance communication in the reproductive behaviors of crayfish (Orconectes quinebaugensis). First, we hypothesized that male crayfish would show stronger attraction towards virgin females (females with no viable sperm) than towards non-virgin females because of the fitness costs (to males) associated with sperm competition. Second, we hypothesized that female crayfish should show differential responses to mature male signals depending on their own sexual history: virgin females should be more strongly attracted to male signals than should non-virgin females because they must mate at least once to be able to fertilize eggs in the spring. Data from two Y-maze experiments yielded support for both hypotheses: males were attracted to signals from virgin females, but not to signals from non-virgins. Likewise, virgin females were attracted to signals from males, but non-virgin females were not. We discuss our data in the context of the potential costs and benefits of mate searching and suggest that distance chemical communication of sexual status may be particularly advantageous when the costs of mate searching are high.

Genetic and morphological evidence for substantial hidden biodiversity in a freshwater crayfish species complex.

North America is a center of biodiversity for freshwater crayfish, with >300 described species, mostly in the family Cambaridae. However, the phylogenetic and phylogeographic relationships among these taxa are poorly understood, despite their ubiquitous occurrence in North American freshwater habitats. Here, we target the geographically widespread Orconectesvirilis and its sister taxa for genetic and morphological investigation. We used sequence data from two mitochondrial genes (16S rRNA and cytochrome oxidase I) and from one nuclear gene (glyceraldehyde-3-phosphate dehydrogenase), as well as morphological data from the male gonopod, to gain insights into phylogenetic relationships among individuals collected in the northeastern United States, where this taxon is considered to be invasive, and from Kansas. Our data reveal evidence for three cryptic species in our collections, in addition to O.virilis sensu stricto; all four clades are separated by both mitochondrial and nuclear sequence data. In addition, two of the newly discovered species, O.sp. nov. A and O.sp. nov. B, are distinguishable from O.virilis by significant differences in gonopod morphology (no data on gonopod morphology were available for O.sp. nov. C). O.sp. nov. A was collected at numerous sites in Massachusetts; additional sampling is required to determine if this species is native to New England. Two other taxa, O.sp. nov. B and O.sp. nov. C, were both collected from sites in eastern Kansas, and historically have probably been considered to be O.nais. In summary, this investigation indicates that this species complex may harbor a great deal of unknown biodiversity over the rest of its described range, and suggests that further attention to the phylogenetics and phylogeography of North American crayfishes may yield interesting insights into the evolution of biodiversity.

Cryptic biodiversity and phylogeographical patterns in a snapping shrimp species complex.

Recent investigations suggest that marine biodiversity may be much higher than earlier estimates, and an important hidden source of diversity in marine systems is the phenomenon of cryptic species complexes. Such complexes are informative models for research into the evolutionary processes that govern species compositions of marine fauna. The snapping shrimp genera Alpheus and Synalpheus are known to harbour large numbers of cryptic species; here, I characterize the genetic structure of the Alpheus armillatus species complex in the northern Caribbean, west Atlantic, and Gulf of Mexico using mitochondrial and nuclear sequence data. Over this geographical region, the complex harbours at least three lineages that are probable reproductively isolated species; all major lineages diverged subsequent to the close of the Isthmus of Panama. Only one lineage was present in the Gulf of Mexico, whereas outside the Gulf of Mexico there was no clear tendency for lineage dominance by geographical region, as most sites were populated by shrimp from at least two lineages. However, within each lineage, there was strong evidence of population genetic differentiation between geographical regions. All lineages showed strong signals of demographic expansion, and one lineage showed sharply reduced genetic diversity, suggestive of past population bottlenecks or recently founded populations with low gene flow from other sites. These results show that evolutionary processes leading to divergence and speciation have been common and recent in the snapping shrimp, and suggest that connectivity among shrimp populations may be limited.

Large differences between LINE-1 amplification rates in the human and chimpanzee lineages.

The genomic evolution and causes of phenotypic variation among humans and great apes remain largely unknown, although the phylogenetic relationships among them have been extensively explored. Previous studies that focus on differences at the amino acid and nucleotide sequence levels have revealed a high degree of similarity between humans and chimpanzees, suggesting that other types of genomic change may have contributed to the relatively large phenotypic differences between them. For example, the activity of long interspersed element 1 (LINE-1) retrotransposons may impose significant changes on genomic structure and function and, consequently, on phenotype. Here we investigate the relative rates of LINE-1 amplification in the lineages leading to humans, bonobos (Pan paniscus), and chimpanzees (P. troglodytes). Our data indicate that LINE-1 insertions have accumulated at significantly greater rates in bonobos and chimpanzees than in humans, provide insights into the timing of major LINE-1 amplification events during great ape evolution, and identify a Pan-specific LINE-1 subfamily.