Phylogeography of the coronulid barnacle, Chelonibia testudinaria, from loggerhead sea turtles, Caretta caretta

Epibiotic fauna of the Antarctic minke whale as a reliable indicator of seasonal movements

Antarctic minke whales, Balaenoptera bonaerensis, breed in tropical and temperate waters of the Southern Hemisphere in winter and feed in Antarctic grounds in the austral summer. These seasonal migrations could be less defined than those of other whale species, but the evidence is scanty. We quantitatively describe the epibiotic fauna of Antarctic minke whales and explore its potential to trace migrations. Seven species were found on 125 out of 333 examined Antarctic minke whales captured during the last Antarctic NEWREP-A expedition in the Southern Ocean: the amphipod Balaenocyamus balaenopterae (prevalence = 22.2%), the copepod Pennella balaenoptera (0.6%); three coronulid, obligate barnacles, Xenobalanus globicipitis (11.1%), Coronula reginae (8.7%), C. diadema (0.9%); and two lepadid, facultative barnacles, Conchoderma auritum (9.0%) and C. virgatum (0.3%). Species with prevalence > 8% exhibited a modest increase in their probability of occurrence with whale body length. Data indicated positive associations between coronulid barnacles and no apparent recruitment in Antarctic waters. All specimens of X. globicipitis were dead, showing progressive degradation throughout the sampling period, and a geographic analysis indicated a marked drop of occurrence where the minimum sea surface temperature is < 12 °C. Thus, field detection -with non-lethal methodologies, such as drones- of coronulid barnacles, especially X. globicipitis, on whales in the Southern Ocean could evince seasonal migration. Future investigations on geographical distribution, growth rate, and degradation (for X. globicipitis) could also assist in timing whales' migration.

Evidence for Host Selectivity and Specialization by Epizoic Chelonibia Barnacles Between Hawksbill and Green Sea Turtles

Epibionts are organisms that utilize the exterior of other organisms as a living substratum. Many affiliate opportunistically with hosts of different species, but others specialize on particular hosts as obligate associates. We investigated a case of apparent host specificity between two barnacles that are epizoites of sea turtles and illuminate some ecological considerations that may shape their host relationships. The barnacles Chelonibia testudinaria and Chelonibia caretta, though roughly similar in appearance, are separable by distinctions in morphology, genotype, and lifestyle. However, though each is known to colonize both green (Chelonia mydas) and hawksbill (Eretmochelys imbricata) sea turtles, C. testudinaria is &gt;5 times more common on greens, while C. caretta is &gt;300 times more common on hawksbills. Two competing explanations for this asymmetry in barnacle incidence are either that the species’ larvae are spatially segregated in mutually exclusive host-encounter zones or their distributions overlap and the larvae behaviorally select their hosts from a common pool. We indirectly tested the latter by documenting the occurrence of adults of both barnacle species in two locations (SE Florida and Nose Be, Madagascar) where both turtle species co-mingle. For green and hawksbill turtles in both locations (Florida: n = 32 and n = 275, respectively; Madagascar: n = 32 and n = 125, respectively), we found that C. testudinaria occurred on green turtles only (percent occurrence – FL: 38.1%; MD: 6.3%), whereas the barnacle C. caretta was exclusively found on hawksbill turtles (FL: 82.2%; MD: 27.5%). These results support the hypothesis that the larvae of these barnacles differentially select host species from a shared supply. Physio-biochemical differences in host shell material, conspecific chemical cues, external microbial biofilms, and other surface signals may be salient factors in larval selectivity. Alternatively, barnacle presence may vary by host micro-environment. Dissimilarities in scute structure and shell growth between hawksbill and green turtles may promote critical differences in attachment modes observed between these barnacles. In understanding the co-evolution of barnacles and hosts it is key to consider the ecologies of both hosts and epibionts in interpreting associations of chance, choice, and dependence. Further studies are necessary to investigate the population status and settlement spectrum of barnacles inhabiting sea turtles.

Epibiont Assemblages on Nesting Hawksbill Turtles Show Site-Specificity in the Persian Gulf

Sea turtle epibionts can provide insights into the hosts' habitat use. However, at present, there is a lack of information on sea turtle epibiont communities in many locations worldwide. Here, we describe the epibiont communities of 46 hawksbill turtles (Eretmochelys imbricata) in the Persian Gulf. Specifically, we sampled 28 turtles from the Dayyer-Nakhiloo National Park (DNNP) in the northern Gulf and 18 turtles from Shibderaz beach in the Strait of Hormuz. A total of 54 macro, meio, and micro-epibiont taxa were identified, including 46 taxa from Shibderaz and 29 taxa from DNNP. The barnacles Chelonibia testudinaria and Platylepas hexastylos, as well as harpacticoid copepods and Rotaliid foraminifers, had the highest frequency of occurrence found on almost all turtle individuals. Harpacticoids were the most abundant epizoic taxa (19.55 ± 3.9 ind. per 9 cm2) followed by forams (Quinqueloculina spp.: 6.25 ± 1.5 ind. per 9 cm2 and Rotaliids: 6.02 ± 1.3 ind. per 9 cm2). Our results showed significant differences between the study sites in the composition of micro and macro-epibiont communities found on hawksbill turtles. We speculate that the differences in epibiont communities were largely influenced by local environmental conditions.

Diversity of intertidal, epibiotic, and fouling barnacles (Cirripedia, Thoracica) from Gujarat, northwest India

The present work studied the diversity of intertidal, epibiotic, and fouling barnacles in the state of Gujarat, northwest India. In total, eleven species belonging to eight genera and five families were recorded in the present study. The Arabian intertidal species Tetraclitaehsani Shahdadi, Chan & Sari, 2011 and Chthamalusbarnesi Achituv & Safriel, 1980 are common in the high- and mid-intertidal rocky shores of Gujarat suggesting that the Gujarat barnacle assemblages are similar to the assemblages in the Gulf of Oman Ecoregion. The biogeographical boundary between the Gulf of Oman and Western Indian ecoregions for barnacles should probably extend southward towards the waters adjacent to Mumbai, where Indo-Pacific species of intertidal barnacles dominate. This study provides the first reports of the common widely distributed balanomorph barnacles Striatobalanustenuis (Hoek, 1883), Tetraclitellakarandei Ross, 1971, Amphibalanusreticulatus (Utinomi, 1967), and lepadid barnacle Lepasanatifera Linnaeus, 1758 in Gujarat, as well as of the chthamalid barnacle Chthamalusbarnesi in India.

Epidemiology of blood flukes (Digenea: Spirorchiidae) in sea turtles from Tyrrhenian and Adriatic Seas, off Italy

Background

The Spirorchiidae is a family of blood flukes parasitizing turtles. Spirorchiids may cause a wide range of inflammatory reactions in the vascular system of their host being frequently implicated with stranding and death of sea turtles worldwide. Recent studies revealed the presence of two spirorchiid species in the Mediterranean basin. Our study presents comparative epidemiological data of spirorchiid infections in loggerhead turtles (Caretta caretta) stranded during an eight-year period from Adriatic and Tyrrhenian Seas, and the first report of Neospirorchis Neogen-11 in a green turtle (Chelonia mydas).

Methods

We screened a total of 319 carcasses of loggerhead turtles stranded from January 2011 to December 2018 along the Tyrrhenian coast (n = 111) and the north-western Adriatic coast (n = 208) of Italy using traditional (copromicroscopy and histopathology) and molecular assays. Three green turtles from the Tyrrhenian coast were also included in the study.

Results

A total of 56 (17.5%) loggerhead turtles and one green turtle (33.3%) were found to be infected with spirorchiid flukes. Amplification, sequencing of the ITS2 region of the ribosomal RNA gene cluster and BLAST analysis confirmed the presence of Hapalotrema mistroides and Neospirorchis Neogen-11 in 51 (16.0%) and 24 (7.5%) loggerhead turtles, respectively, and Neospirorchis Neogen-11 in an infected green turtle. Differences in prevalence of infection between the two sampling areas were found.

Conclusions

The risk of spirorchiid infection in the Tyrrhenian Sea is lower than in the Adriatic Sea and in general the risk of infection in the Mediterranean is lower than in other geographical locations. Differences in the prevalence of infection between the two sampling areas were related to the differences of regional habitats supporting different abundance of spirorchiid intermediate hosts. A systematic monitoring to evaluate the progress of the infection is recommended, as well as studies on the occurrence and distribution of spirorchiid species from other Mediterranean areas.

Parallel Patterns of Host-Specific Morphology and Genetic Admixture in Sister Lineages of a Commensal Barnacle

Symbiotic relationships are often species specific, allowing symbionts to adapt to their host environments. Host generalists, on the other hand, have to cope with diverse environments. One coping strategy is phenotypic plasticity, defined by the presence of host-specific phenotypes in the absence of genetic differentiation. Recent work indicates that such host-specific phenotypic plasticity is present in the West Pacific lineage of the commensal barnacle Chelonibia testudinaria (Linnaeus, 1758). We investigated genetic and morphological host-specific structure in the genetically distinct Atlantic sister lineage of C. testudinaria. We collected adult C. testudinaria from loggerhead sea turtles, horseshoe crabs, and blue crabs along the eastern U.S. coast between Delaware and Florida and in the Gulf of Mexico off Mississippi. We find that shell morphology, especially shell thickness, is host specific and comparable in similar host species between the Atlantic and West Pacific lineages. We did not detect significant genetic differentiation related to host species when analyzing data from 11 nuclear microsatellite loci and mitochondrial sequence data, which is comparable to findings for the Pacific lineage. The most parsimonious explanation for these parallel patterns between distinct lineages of C. testudinaria is that C. testudinaria maintained phenotypic plasticity since the lineages diverged 4-5 mya.

Microsatellite loci discovery from next-generation sequencing data and loci characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758)

Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758). Chelonibia testudinaria appears to be a host generalist, and has an unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable markers, such as microsatellite markers. In the present study, we discovered thousands of new microsatellite loci from next-generation sequencing data, and characterized 12 loci thoroughly. We conclude that 11 of these loci will be useful markers in future ecological and evolutionary studies on C. testudinaria.

Two new species of the gorgonian inhabiting barnacle, Conopea (Crustacea, Cirripedia, Thoracica), from the Gulf of Guinea

Two new species of Conopea (Say 1822) are described from the Gulf of Guinea: Conopea saotomensis sp. n.and Conopea fidelis sp. n. These two new species were collected from the historically isolated volcanic islands of São Tomé and Príncipe. The relationship between Conopea saotomensis sp. n., Conopea fidelis sp. n.and two other Atlantic barnacle species, Conopea calceola (Ellis 1758) and Conopea galeata (Linnaeus 1771), is examined. The methods employed are the construction of a molecular phylogeny using mitochondrial COI and nuclear H3 gene sequence data along with morphological comparisons of calcareous and cuticular body parts. It is found that Conopea saotomensis sp. n., Conopea fidelis sp. n.and Conopea calceola are most closely related to each other but the relationship among them is unresolved. Gorgonian hosts are identified. Preliminary observations show species level host specificity for Conopea fidelis sp. n.

Host-specific phenotypic plasticity of the turtle barnacle Chelonibia testudinaria: a widespread generalist rather than a specialist

Turtle barnacles are common epibionts on marine organisms. Chelonibia testudinaria is specific on marine turtles whereas C. patula is a host generalist, but rarely found on turtles. It has been questioned why C. patula, being abundant on a variety of live substrata, is almost absent from turtles. We evaluated the genetic (mitochondrial COI, 16S and 12S rRNA, and amplified fragment length polymorphism (AFLP)) and morphological differentiation of C. testudinaia and C. patula from different hosts, to determine the mode of adaptation exhibited by Chelonibia species on different hosts. The two taxa demonstrate clear differences in shell morphology and length of 4-6(th) cirri, but very similar in arthropodal characters. Moreover, we detected no genetic differentiation in mitochondrial DNA and AFLP analyses. Outlier detection infers insignificant selection across loci investigated. Based on combined morphological and molecular evidence, we proposed that C. testudinaria and C. patula are conspecific, and the two morphs with contrasting shell morphologies and cirral length found on different host are predominantly shaped by developmental plasticity in response to environmental setting on different hosts. Chelonibia testudinaria is, thus, a successful general epibiotic fouler and the phenotypic responses postulated can increase the fitness of the animals when they attach on hosts with contrasting life-styles.

Dwarf males of Octolasmis warwickii (Cirripedia: Thoracica): the first example of coexistence of males and hermaphrodites in the suborder Lepadomorpha

In the lepadomorph barnacle Octolasmis warwickii, individuals are often found attached to the scutum of conspecifics living externally on the crab hosts. To test whether these conspecific-attached individuals are dwarf males, as are known to occur in other suborders of barnacles, we compared the pattern of attachment, size-frequency distribution, and reproductive status of the conspecific-attached (Con-A) and crab-attached (Crab-A) individuals. Con-As were smaller than Crab-As. There was a positive relationship between the body size of Crab-As and the number of individuals on them. Con-As had longer penises than Crab-As of the same body size, and their testes were better developed. The four largest Con-As examined were brooding eggs. These results indicate that Con-As of O. warwickii are dwarf males, with a potential to become hermaphroditic. This represents the first known example of coexistence of males and hermaphrodites in the suborder Lepadomorpha. The mating group size of O. warwickii was smaller than in its hermaphroditic congeners but larger than in barnacles with dwarf males and females, which supports the current theories that group size is important for the evolution of sexuality patterns in barnacles.

Population genetics and phylogeography of sea turtles

The seven species of sea turtles occupy a diversity of niches, and have a history tracing back over 100 million years, yet all share basic life-history features, including exceptional navigation skills and periodic migrations from feeding to breeding habitats. Here, we review the biogeographic, behavioural, and ecological factors that shape the distribution of genetic diversity in sea turtles. Natal homing, wherein turtles return to their region of origin for mating and nesting, has been demonstrated with mtDNA sequences. These maternally inherited markers show strong population structure among nesting colonies while nuclear loci reveal a contrasting pattern of male-mediated gene flow, a phenomenon termed 'complex population structure'. Mixed-stock analyses indicate that multiple nesting colonies can contribute to feeding aggregates, such that exploitation of turtles in these habitats can reduce breeding populations across the region. The mtDNA data also demonstrate migrations across entire ocean basins, some of the longest movements of marine vertebrates. Multiple paternity occurs at reported rates of 0-100%, and can vary by as much as 9-100% within species. Hybridization in almost every combination among members of the Cheloniidae has been documented but the frequency and ultimate ramifications of hybridization are not clear. The global phylogeography of sea turtles reveals a gradient based on habitat preference and thermal regime. The cold-tolerant leatherback turtle (Dermochelys coriacea) shows no evolutionary partitions between Indo-Pacific and Atlantic populations, while the tropical green (Chelonia mydas), hawksbill (Eretmochelys imbricata), and ridleys (Lepidochelys olivacea vs. L. kempi) have ancient separations between oceans. Ridleys and loggerhead (Caretta caretta) also show more recent colonization between ocean basins, probably mediated by warm-water gyres that occasionally traverse the frigid upwelling zone in southern Africa. These rare events may be sufficient to prevent allopatric speciation under contemporary geographic and climatic conditions. Genetic studies have advanced our understanding of marine turtle biology and evolution, but significant gaps persist and provide challenges for the next generation of sea turtle geneticists.

Testing dispersal and cryptic diversity in a widely distributed groundwater amphipod (Niphargus rhenorhodanensis)

Theories about colonization and evolution in groundwater have assumed that the fragmented structure of groundwater strongly limits dispersal. The high number of endemic and allopatric species in groundwater supports this hypothesis, but the occurrence of widely distributed groundwater taxa calls into question its universality. These widely distributed taxa might also be sets of cryptic species because extreme conditions of life in groundwater promote cryptic diversity by inducing convergent morphological evolution. Niphargus rhenorhodanensis is a widely distributed and ubiquitous groundwater amphipod which supposedly colonized the Alps after Quaternary glaciations. We tested the dispersal and the cryptic species hypotheses within this species using a phylogeographic approach based on two mitochondrial genes (COI and 16S) and a nuclear gene (28S). Results support the view that poor dispersal is a main evolutionary factor in groundwater. All genes independently supported the existence of numerous cryptic and mostly allopatric units within N. rhenorhodanensis, indicating that its apparently wide distribution range is an artefact generated by cryptic diversity. We reject the hypothesis of a recent and global colonization of the Alps and argue that some N. rhenorhodanensis lineages probably survived glaciations near or within the Alps.

Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation

With today's technology for production of molecular sequences, DNA taxonomy and barcoding arose as a new tool for evolutionary biology and ecology. However, their validities still need to be empirically evaluated. Of most importance is the strength of the correlation between morphological taxonomy and molecular divergence and the possibility to define some molecular thresholds. Here, we report measurements of this correlation for two mitochondrial genes (COI and 16S rRNA) within the sub-phylum Crustacea. Perl scripts were developed to ensure objectivity, reproducibility, and exhaustiveness of our tests. Our analysis reveals a general correlation between molecular divergence and taxonomy. This correlation is particularly high for shallow taxonomic levels allowing us to propose a COI universal crustacean threshold to help species delimitation. At higher taxonomic levels this correlation decreases, particularly when comparing different families. Those results plead for DNA use in taxonomy and suggest an operational method to help crustacean species delimitation that is linked to the phylogenetic species definition. This pragmatic tool is expected to fine tune the present classification, and not, as some would have believed, to tear it apart.

Nuclear markers confirm taxonomic status and relationships among highly endangered and closely related right whale species

Right whales (genus: Eubalaena) are among the most endangered mammals, yet their taxonomy and phylogeny have been questioned. A phylogenetic hypothesis based on mitochondrial DNA (mtDNA) variation recently prompted a taxonomic revision, increasing the number of right whale species to three. We critically evaluated this hypothesis using sequence data from 13 nuclear DNA (nuDNA) loci as well as the mtDNA control region. Fixed diagnostic characters among the nuclear markers strongly support the hypothesis of three genetically distinct species, despite lack of any diagnostic morphological characters. A phylogenetics analysis of all data produced a strict consensus cladogram with strong support at nodes that define each right whale species as well as relationships among species. Results showed very little conflict among the individual partitions as well as congruence between the mtDNA and nuDNA datasets. These data clearly demonstrate the strength of using numerous independent genetic markers during a phylogenetics analysis of closely related species. In evaluating phylogenetic support contributed by individual loci, 11 of the 14 loci provided support for at least one of the nodes of interest to this study. Only a single marker (mtDNA control region) provided support at all four nodes. A study using any single nuclear marker would have failed to support the proposed phylogeny, and a strong phylogenetic hypothesis was only revealed by the simultaneous analysis of many nuclear loci. In addition, nu DNA and mtDNA data provided complementary levels of support at nodes of different evolutionary depth indicating that the combined use of mtDNA and nuDNA data is both practical and desirable.

Geographic genetic architecture of pocket gopher (Thomomys bottae) populations in Baja California, Mexico

Phylogenetic analyses of complete mitochondrial cytochrome b sequences support the monophyly of pocket gopher (Thomomys bottae) populations from the 1000 km length of the Baja California peninsula of Mexico, relative to other geographical segments of the species range in western North America. The Baja California peninsula is an area that encompasses considerable ecomorphological and infraspecific diversity within this pocket gopher species. However, detailed population analyses encompassing 35 localities distributed over the southern half of the peninsula reveal only trivial phylogeographical structure. Rather, most of the 72 unique 500-base pair haplotypes examined from 142 individuals is restricted to single populations, although a few haplotypes are shared broadly across geography. Individual populations are typically comprised of haplotype sets from different branches in a network of relationships. Analysis of molecular variance (amova) indicates that approximately half of the total pool of variation is contained among individuals within local populations, and that only about 25% can be explained by the regional subdivisions of current subspecies distributions or physiographic realms. A hypothesized historical vicariant event that has been causally linked to the phylogeographical structure of other, codistributed species has had little influence on these pocket gopher populations, explaining only 13% of the total variation. The temporal depth, estimated by coalescence parameters, of the haplotype lineage in Baja California is relatively recent, approximately 300,000 generations; both the mismatch distribution of pairwise comparisons and a significantly positive exponential growth estimate support a recent history of expanding populations; but current, or recent past, migration estimates have remained small, are largely unidirectional from north to south, and weak isolation by distance is present. All data suggest that pocket gophers have relatively recently invaded the southern half of peninsular Baja California, with the genetic signature of expansion still evident but with sufficient time having lapsed to result in a weak isolation by distance pattern. The geographical assemblage of sampled populations thus appears as a meta-population, with limited gene flow contrasting with random haplotype loss due to drift in small, localized populations.

Evaluating the performance of likelihood methods for detecting population structure and migration

A plethora of statistical models have recently been developed to estimate components of population genetic history. Very few of these methods, however, have been adequately evaluated for their performance in accurately estimating population genetic parameters of interest. In this paper, we continue a research program of evaluation of population genetic methods through computer simulation. Specifically, we examine the software MIGRATEE-N 1.6.8 and test the accuracy of this software to estimate genetic diversity (Theta), migration rates, and confidence intervals. We simulated nucleotide sequence data under a neutral coalescent model with lengths of 500 bp and 1000 bp, and with three different per site Theta values of (0.00025, 0.0025, 0.025) crossed with four different migration rates (0.0000025, 0.025, 0.25, 2.5) to construct 1000 evolutionary trees per-combination per-sequence-length. We found that while MIGRATEE-N 1.6.8 performs reasonably well in estimating genetic diversity (Theta), it does poorly at estimating migration rates and the confidence intervals associated with them. We recommend researchers use this software with caution under conditions similar to those used in this evaluation.