Genomic atolls of differentiation in coral reef fishes (Hypoplectrus spp., Serranidae)

Because the vast majority of species are well diverged, relatively little is known about the genomic architecture of speciation during the early stages of divergence. Species within recent evolutionary radiations are often minimally diverged from a genomic perspective, and therefore provide rare opportunities to address this question. Here, we leverage the hamlet radiation (Hypoplectrus spp., brightly coloured reef fishes from the tropical western Atlantic) to characterize genomic divergence during the early stages of speciation. Transect surveys and spawning observations in Belize, Honduras and Panama confirm that sympatric barred (H. puella), black (H. nigricans) and butter (H. unicolor) hamlets are phenotypically distinct and reproductively isolated, although hybrid spawnings and individuals with intermediate phenotypes are seen on rare occasions. A survey of approximately 100 000 restriction site‐associated SNPs in 126 samples from the three species across the three replicate populations reveals extremely slight genomewide divergence among species (F_ST = 0.0038), indicating that ecomorphological differences and functional reproductive isolation are maintained in sympatry in a backdrop of extraordinary genomic similarity. Nonetheless, a very small proportion of SNPs (0.05% on average) are identified as F_ST outliers among sympatric species. Remarkably, a single SNP is identified as an outlier in repeated populations for the same species pair. A minicontig assembled de novo around this SNP falls into the genomic region containing the HoxCa10 and HoxCa11 genes in 10 teleost species, suggesting an important role for Hox gene evolution in this radiation. This finding, if confirmed, would provide a better understanding of the links between micro‐ and macroevolutionary processes.     

Ecological differences between hamlet (Hypoplectrus: Serranidae) colour morphs: between-morph variation in diet

Dietary differences between hamlet Hypoplectrus spp. colour morphs were examined in fishes from Puerto Rico, U.S. Virgin Islands, Curacao, Honduras and Belize. Hamlet diet across all countries was characterized by large overlap between most colour morphs in both the proportion and numbers of dietary items consumed, although some differences between morphs were apparent. Indigo hamlets Hypoplectrus indigo were the only morph to consume fishes (blue chromis Chromis cyanea and sunshinefish Chromis insolata ) almost exclusively. The sympatric occurrence of other ecologically indistinguishable colour morphs, however, suggests that divergent ecological selection alone cannot explain population divergence in hamlets. Geographical variation in diet was also observed within black Hypoplectrus nigricans and yellowtail Hypoplectrus chlorurus hamlets which may reflect geographical differences in prey availability or differences in prey choice.     

Population genomics of local adaptation versus speciation in coral reef fishes (Hypoplectrus spp,Serranidae)

Are the population genomic patterns underlying local adaptation and the early stages of speciation similar? Addressing this question requires a system in which (i) local adaptation and the early stages of speciation can be clearly identified and distinguished, (ii) the amount of genetic divergence driven by the two processes is similar, and (iii) comparisons can be repeated both taxonomically (for local adaptation) and geographically (for speciation). Here, we report just such a situation in the hamlets (Hypoplectrus spp), brightly colored reef fishes from the wider Caribbean. Close to 100,000 SNPs genotyped in 126 individuals from three sympatric species sampled in three repeated populations provide genome‐wide levels of divergence that are comparable among allopatric populations (F_st estimate = 0.0042) and sympatric species (F_st estimate = 0.0038). Population genetic, clustering, and phylogenetic analyses reveal very similar patterns for local adaptation and speciation, with a large fraction of the genome undifferentiated (F_st estimate ≈ 0), a very small proportion of F_st outlier loci (0.05–0.07%), and remarkably few repeated outliers (1–3). Nevertheless, different loci appear to be involved in the two processes in Hypoplectrus, with only 7% of the most differentiated SNPs and outliers shared between populations and species comparisons. In particular, a tropomyosin (Tpm4) and a previously identified hox (HoxCa) locus emerge as candidate loci (repeated outliers) for local adaptation and speciation, respectively. We conclude that marine populations may be locally adapted notwithstanding shallow levels of genetic divergence, and that from a population genomic perspective, this process does not appear to differ fundamentally from the early stages of speciation.     

No barriers to fertilization between sympatric colour morphs in the marine species flock Hypoplectrus (Serranidae)

Assortative mate choice is, so far, the only demonstrated isolating barrier between colour morphs in fish species flocks, such as freshwater cichlids and marine hamlets, suggesting an important role for sexual selection in speciation. However, there has been little consideration of post-copulatory mechanisms that are known to influence reproductive isolation in other taxa. Selective pressures through a cost to hybrid matings, or genetic drift, may lead to the evolution of fertilization barriers through gamete incompatability. In cases of incipient speciation, such as the hamlets, complete fertilization blocks may not have evolved. Instead, differential fertilization between species may reduce the success of interspecific fertilizations. We examined the fertilization dynamics of sympatric Hypoplectrus nigricans (black hamlet) and Hypoplectrus puella (barred hamlet). Experimental crosses were performed to score fertilization success in within-morph and between-morph crosses. Fertilization success did not differ between self-fertilized, within-morph or between-morph crosses. We therefore found no evidence of post-mating barriers through sperm:egg incompatibilities and potential for self-fertilization. Our results are consistent with a mechanism of colour morph divergence based on sexually selected morph mating preferences.     

Site Variation in Spatial Aggregation and Phorophyte Preference in Psychilis monensis (Orchidaceae)

Aggregation patterns of plants vary according to spatial scale and developmental stage, and are dependent on vegetation dynamics and species composition. We describe the aggregation patterns of the epiphytic orchid Psychilis monensis from two sites with different vegetation structure and composition on Mona Island, Puerto Rico. We analyzed spatial variation for seedlings, juveniles, and adults using the density-independent, standardized Morisita index (I_MS). We censused a total of 879 plants. Strong preferences for some phorophyte species were evident, including dead trees, but association with bark roughness was equivocal. The highest densities occurred in the site with the lowest fruit and seed production, suggesting that the best sites for pollination and seedling establishment were not the same. Seedlings at one site were significantly aggregated, but all other stages were indistinguishable from a random distribution. Nevertheless, adults at both sites had the lowest I_MS values indicating that they tend to be the least aggregated of the three life history stages. The abundance and age structure of P. monensis were clearly affected by the frequency of their preferred hosts, but site-specific factors affecting seedling survival probably play a major role in site differences.     

Influence of a simulated hurricane on aquatic insect recolonization in the phytotelma of Heliconia caribaea (Heliconiacaea)

Disturbances like hurricanes can affect diversity and community composition, which may in turn affect ecosystem function. We examined how a simulated hurricane disturbance affected insect communities inhabiting the phytotelma (plant-held waters) of Heliconia caribaea in the Luquillo Experimental Forest of eastern Puerto Rico, a tropical island that frequently experiences hurricanes. We hypothesized that disturbance would alter diversity and that larger Heliconia would attract more species following disturbance due to the area-diversity relationship described by the Theory of Island Biogeography. Individual flower parts (bracts) of Heliconia inflorescences (racemes) were artificially disturbed via removal of existing insect communities, then after refilling with water, cohorts of Heliconia were destructively sampled biweekly for 6 weeks to assess recolonization patterns of α (bract level), β, and γ (summed across bracts; raceme level) diversity over time and across raceme sizes. Although we found no support for our hypothesis about the effect of raceme size on recolonization, our hypothesis regarding recolonization patterns over time was supported; species richness, evenness, and abundance of bracts increased directly after the disturbance and then decreased below pre-disturbance levels, and community composition at the raceme level changed significantly over time during recolonization. β Diversity was also greater in smaller racemes compared to larger racemes, suggesting high heterogeneity across bracts of Heliconia racemes exacerbated by raceme size and age. Overall, our results highlight the importance of scale and appropriate measurements of diversity (particularly α) in experiments aiming to extrapolate conclusions about the ecological impacts of disturbances across different habitats and ecosystems.     

Chromosomes of some Puerto Rican flea beetles (Coleoptera: Chrysomelidae: Alticinae): multiple cytogenetic evolutionary tendencies in the neotropics

Meiotic chromosomes of 10 West Indian flea beetles with restricted distribution, including eight Puerto Rican endemics, were studied. Two species of the cosmopolitan Longitarsus resemble Old World congenerics in having meioformulae 13 + Xy and 14 + Xy, both with one pair of enlarged autosomes. One unidentified species of Aphthona seems to have achiasmatic meiosis. Among the Puerto Rican endemics, repeated fusions have produced low-numbered karyotypes in Homoschema latitarsum (2 + neoXY, now the lowest meioformula known for the Chrysomelidae) and Heikertingerella krugi (4 + neoXY). Three species of Aedmon have 18 + Xy_p as a result of a series of centric fissions from the Polyphagan ancestral condition of nine pairs. Phyllotrupes sp. (a new genus record for Puerto Rico, near P. acutangula ) and Pseudodisonycha portoricensis have 17 + Xy and 16 + Xy, respectively, plus a swarm of supernumerary chromosomes.     

Intracardiac and aortic thrombi in capuchin monkeys (Cebus apella)

Massive intracardiac or aortic mural thrombi, probably of septic origin, occurred in six capuchin monkeys (Cebus apella) and accounted for 26% of all adult deaths in a breeding group over a 4-yr period. Previous experimental inoculations with herpes simplex type 2 virus may have contributed to the development of these fatal lesions.     

Biology of the Mongoose (Herpestes javanicus) in a Rain Forest of Puerto Rico1

Ecological aspects of the mongoose (Herpestes javanicus) were studied in the Luquillo Mountains, a rain forest region in eastern Puerto Rico. Information was obtained by removal trapping of mongoose from grids placed in tree plantations, colorado and tabonuco forests. Trapping efficiency was two mongoose per 100 trap-days, suggesting mongoose abundance is low in wet montane forests of Puerto Rico. Sex ratio was biased (2.6:1) in favor of males. Body masses of male mongoose inhabiting rain forests of the Luquillo Mountains were larger than those in dry forests at Guánica (P < 0.0001). Stomach contents from 18 mongoose were examined, animal matter comprised 75 percent of the total food items encountered. Of these, 33 percent were from vertebrates. The food items most frequently encountered were lizards (Anolis spp.), centipedes (Scolopendra spp.), and cockroaches (Blatellidae).     

Adult Polycystic Kidney Disease in a Rhesus Monkey (Macaca mulatta)

Adult polycystic kidney disease was diagnosed at necropsy in a 16-year-old rhesus monkey dead from renal failure. Both kidneys were enlarged and contained multiple cysts ranging from 0.1 to 4.0 cm in diameter. The age of onset of the clinical signs, terminal uremia, and the gross and histologic findings in this macaque were consistent with adult (type III) polycystic kidney disease of man.     

Disease of Red Mangrove (Rhizophora mangley) in Southwest Puerto Rico Caused by Cytospora rhizophorae1

A high frequency of dieback and mortality was found in Rhizophora mangle (red mangrove) in coastal mangrove forests of southwest Puerto Rico. Eight plots were established in a variety of mangrove environments to assess the extent and severity of the dieback and mortality. The imperfect fungus Cytospora rhizopborae was isolated consistently from stem dieback and associated canker tissues. No other pathogenic microorganisms were isolated. Pathogenicity was demonstrated in greenhouse and field inoculation experiments with C. rhizophorae using young R. mangle seedlings. In field studies of seedlings inoculated, mortality was 33 percent, and greenhouse mortality was as high as 50 percent. Cytospora rhizophorae was isolated consistently from diseased mangrove tissue; the fungus was grown in pure culture and then inoculated into healthy red mangroves, causing cankers. Koch's postulates were fulfilled by infecting R. mangle with C. rhizophorae, producing disease symptoms, and successfully re‐isolating C. rhizophorae from the diseased tissue. This is the first documentation of the pathogenicity of C. rhizophorae associated with mortality in red mangrove. In the coastal mangrove forests of southwest Puerto Rico, C. rhizophorae may play an important role in the frequency of dieback and mortality in R. mangle, producing slow stem diameter growth and causing frequent stem and root wounds.     

Temporal changes in abundance–occupancy relationships over 40 years

1. Abundance–occupancy (A–O) relationships are widely documented for many organismal groups and regions, and have been used to gain an understanding of regional population and community trends. Monitoring changes in abundance and occupancy over time may be what is required to document changes in conservation status and needs for some species, communities, or areas.
2. We hypothesize that if there is a higher proportion of declining species in one group of species compared with another (e.g., migratory species vs. permanent residents), then a consequence of that difference will be vastly different abundance–occupancy relationships. If this difference persists through time, then the resulting A–O relationships between the groups will continue to diverge.
3. For neotropical migrants, short‐distance migrants, and permanent resident birds of North America, we assess the numbers of declining species over 1969–2009. We further test for differences in the A–O relationship across these three groups, and in rates of change in abundance and occupancy separately.
4. We find significant differences in numbers of declining species across the migratory groups, a significant decline in the A–O relationship for permanent residents, a significant increase for Neotropical migrants, and a nonsignificant decline for short‐distance migrants over the 40 years. Further, abundances are not changing at different rates but occupancies are consistently greater over time for neotropical migrants versus permanent residents, likely driving the changes in A–O relationships observed.
5. In these analyses, we documented changing A–O trends for different groups of species, over a relatively long time period for ecological studies, one of only a few studies to examine A–O relationships over time. Further, we have shown that a temporally unvarying abundance–occupancy relationship is not universal, and we posit that variability in A–O relationships is due to human impacts on habitats, coupled with variation in species' abilities to respond to human impacts.

     

Differences in composition of macroinvertebrate communities with invasive and native Gammarus spp. (Crustacea: Amphipoda)

SUMMARY 1. Assessing the effects on communities of invasive species is often confounded by environmental factors. In Irish rivers, the introduced amphipod Gammarus pulex replaces the native G. duebeni celticus in lowland stretches. The two amphipods are associated with different macroinvertebrate communities, which may in part be the result of natural longitudinal physicochemical change. However, this hinders assessment of any direct community impacts of the invasive as compared with the native species. Here, we report on a fortuitous circumstance that allowed us to uncouple the community effects of Gammarus species from environmental differences.
2. The lowland stretch of the River Lissan is dissected by a weir, which has slowed the upstream invasion by G. pulex . We took physicochemical measurements and macroinvertebrate samples from three contiguous 150 m reaches of this stretch with G. pulex only, mixed Gammarus and G. d. celticus only communities.
3. We found no biologically significant differences in physicochemistry among the three reaches. Overall invertebrate densities did not differ among reaches. However, G. pulex numerically dominated its reach, whilst G. d. celticus abundance was relatively low in its reach. The G. pulex reach had significantly higher overall biomass because of high invader abundance. In addition, both diversity and species richness of macroinvertebrate communities were lower in the G. pulex than the G. d. celticus reach, with the mixed Gammarus reach intermediate.
4. Ordination indicated distinctly different associations of invertebrate community samples and taxa that were best explained by the distributions of the Gammarus species. Again, the mixed Gammarus species samples were intermediate.
5. This study indicates that the invasive G. pulex has a greater impact on macroinvertebrate community composition than the native G. d. celticus , probably through biotic interactions such as predation.     

Absence of Naturally Acquired Tetanus Antitoxin in the Free-Ranging Cayo Santiago Rhesus Monkeys (Macaca mulatta)

Tetanus is enzootic in the free-ranging rhesus monkey colony on Cayo Santiago. The disease accounts for 25% of all mortalities in the population. The high prevalence of tetanus provided a unique opportunity to study the potential roles of geophagia, wounding, and clinical tetanus infections on the development of naturally acquired tetanus antitoxin in rhesus macaques. Eighty-six unvaccinated monkeys, including six that recovered from tetanus, were serosurveyed using a mouse toxin neutralization test. None of the animals had detectable antitoxin titers (<0.001 AU/ml), suggesting that natural immunity to tetanus is either rare or nonexistent in the Cayo Santiago colony.     

New genus and species of flea beetles (Coleoptera, Chrysomelidae, Galerucinae, Alticini) from Puerto Rico, with comments on flea beetle diversity in the West Indies and a key to the West Indian Monoplatini genera

A new genus (Borinken) and five new species (Borinken elyunque, Distigmoptera chamorrae, Kiskeya elyunque, Ulrica eltoro, and Ulrica iviei) from Puerto Rico are described and illustrated. A keyto all West Indian Monoplatini genera is provided, as are keys to all speciesof Kiskeya and to the speciesof Ulrica from Puerto Rico. A list of the flea beetle genera, along with the number of species and some of the faunal features is presented and discussed for the West Indies.     

Temporal changes of local and regional processes in the assembly of herbivorous insect communities

Herbivorous insect communities are structured by multiple processes operating locally (e.g. bottom–up effects of plants) and regionally (e.g. dispersal limitation). Although the relative strength of these processes has been well documented, how it varies in time is less understood, especially in relation with the temporal dynamics of plant communities. If temporal turnover of local plant species composition is too rapid for insect community assembly to keep up with, bottom–up effects are expected to be weak. Here, in plant and herbivorous insect communities in Japanese grasslands, we studied how the relative importance of local (bottom–up effects of plants, structures of plant communities and top–down effects of predators) and regional (dispersal limitation) processes varies over the growing season. In addition, we tested the hypothesis that larger temporal turnover of plant species composition is related to the weaker bottom–up effects, that is, the lower explanation power of plant communities for insect communities. We found that, throughout the growing season, the insect species composition was mainly explained by local variables (plant species composition, vegetation height and predator abundance), and their explanation power was higher during later phases of the season (late summer). Furthermore, the variation not explained by plant species composition was correlated with the degree of temporal turnover of plants, suggesting that insect communities failed to track the temporal turnover of plant species. These results were pronounced when we focused on leaf sucker insects, whose host plant range is presumably more limited. We conclude that herbivorous insect communities are mainly regulated by local processes, especially bottom–up effects from plants, while stochasticity may have played a role in early phases of the season. Furthermore, we underscore the importance of considering relative time scale of community assembly and environmental shifts, especially in systems characterized by dynamic changes.     

Polymorphic microsatellite loci for the Puerto Rican crested anole (<Emphasis Type="Italic">Anolis cristatellus</Emphasis>) and their amplification in related Puerto Rican species

We isolate six highly polymorphic microsatellite loci for the Puerto Rican crested anole (Anolis cristatellus) from a genomic library enriched for CA repeats. The number of alleles per locus ranged from 14 to 19, with levels of observed heterozygosity ranging from 0.60 to 0.73. Most of these loci were successfully cross-amplified in other members of the cristatellus species group (A. evermanni, A. gundlachi, A. krugi, A. stratulus), but levels of polymorphism were lower.     

Passive joint mobility in patas monkeys (Erythrocebus patas): rehabilitation of caged animals after release into a free-ranging environment

A previous study of passive joint mobility in patas monkeys (Erythrocebus patas) showed that laboratory-caged animals had significantly greater mobility in most joints than age/sex matched free-ranging monkeys. Passive joint mobility on 27 of the same animals was measured 6 months after the caged animals were released onto a 40-hectare island. The results show that within 6 months of becoming free-ranging, typical passive joint mobility is restored. Thus, although caging directly affects measurements of morphologically-determined features in patas monkeys, confinement itself does not necessarily prevent rehabilitation if the immature monkeys are released into a free-ranging environment.