The phylogenetic position of the Critically Endangered Saint Croix ground lizard Ameiva polops: revisiting molecular systematics of West Indian Ameiva.

The phylogenetic position of the critically endangered Saint Croix ground lizard Ameiva polops is presently unknown and several hypotheses have been proposed. We investigated the phylogenetic position of this species using molecular phylogenetic methods. We obtained sequences of DNA fragments of the mitochondrial ribosomal genes 12S rDNA and 16S rDNA for this species. We aligned these sequences with published sequences of other Ameiva species, which include most of the Ameiva species from the West Indies, three Ameiva species from Central America and South America, and one from the teiid lizard Tupinambis teguixin, which was used as outgroup. We conducted Maximum Likelihood and Bayesian phylogenetic analyses. The phylogenetic reconstructions among the different methods were very similar, supporting the monophyly of West Indian Ameiva and showing within this lineage, a basal polytomy of four clades that are separated geographically. Ameiva polops grouped in a cluster that included the other two Ameiva species found in the Puerto Rican Bank: A. wetmorei and A. exsul. A sister relationship between A. polops and A. wetmorei is suggested by our analyses. We compare our results with a previous study on molecular systematics of West Indian Ameiva. 

Cryptic diversity and phylogeographic patterns of Deto echinata (Isopoda: Detonidae) in southern Africa.

Recent phylogeographic studies of poorly-dispersing coastal invertebrates in highly biodiverse regions have led to the discovery of high levels of cryptic diversity and complex phylogeographic patterns that suggest isolation, geological, and ecological processes have shaped their biodiversity. Studies of southern African coastal invertebrates have uncovered cryptic diversity for various taxa and phylogeographic patterns that, although sharing some similarities across taxa, do differ. These findings underscore the need for additional studies to better understand the biodiversity levels, distributional patterns, and processes responsible for producing coastal biodiversity in that region. The coastal isopod Deto echinata is of particular interest, as its complex taxonomic history, poor dispersal capabilities, and broad geographic distribution suggest the potential for cryptic diversity. We use mitochondrial and nuclear sequences to characterize D. echinata individuals from localities ranging from northern Namibia to Glentana, about 2,500 km along the coastline on the south coast of South Africa. These are used to assess whether D. echinata harbors cryptic genetic diversity and whether phylogeographic distributional patterns correlate with those previously documented for other coastal isopods in the region. Analysis of mitochondrial and nuclear sequences revealed two deeply-divergent lineages that exhibit a distributional break in the Cape Peninsula region. These findings suggest D. echinata is a cryptic species complex in need of taxonomic revision and highlight the need for further taxonomic and phylogeographic studies of similarly poorly-dispersing coastal invertebrates in southern Africa.

Cryptic Genetic Diversity in the Coastal Isopod Alloniscus oahuensis from the Pacific Ocean.

The isopod sub-order Oniscidea includes over 3,700 species and is known to occur in all terrestrial environments, except those at extreme elevations and polar latitudes. Current estimates of the biodiversity of the Oniscidea may be underestimates, as recent molecular studies have uncovered high levels of cryptic diversity in several taxa in the sub-order. High levels of cryptic diversity have been found in coastal species, species from remote and isolated regions, and species with complex taxonomic histories. Alloniscus oahuensis is a good candidate to harbor cryptic diversity, as it is a coastal isopod species with a geographic range that spans several remote and isolated archipelagos in the Pacific Ocean and has a complex taxonomic history. In this study, we used sequences for three mitochondrial genes and one nuclear gene to determine whether A. oahuensis harbors highly divergent lineages that may represent cryptic species. By characterizing 60+ A. oahuensis individuals from 17 localities from various Pacific Ocean archipelagos, we uncovered two deeply divergent lineages with disjunct distributions. The levels of genetic divergence observed amongst the two lineages match or exceed those reported across other cryptic species in the Oniscidea, suggesting that A. oahuensis may represent a cryptic species complex in need of a taxonomic revision. The extremely low lineage diversities within A. oahuensis indicate that the lineages may have spread across the Pacific Ocean recently, potentially due to anthropogenic activity.

Redescription of Tylosmaindroni Giordani Soika, 1954 (Crustacea, Isopoda, Oniscidea) based on SEM and molecular data.

The woodlouse species Tylosmaindroni Giordani Soika, 1954 (Crustacea, Isopoda, Oniscidea) is redescribed from the Persian Gulf based on light and scanning electron microscopy. This species differs from the closely related T.exiguus Stebbing, 1910, from the Red Sea (coasts of Sudan and Eritrea), and Socotra Island, by pereopod 1 superior margin without a prominent projection and pleopod 2 endopod 2.3 times as long as exopod, vs. 3.6 in T.exiguus. A distribution map for T.maindroni is provided. In addition, we studied the molecular differentiation of five populations of T.maindroni from the Persian Gulf, based on partial cytochrome c oxidase subunit I (COI) gene sequences. The results revealed low levels of population structuring between the analyzed populations.

First report of lionfish prey from Western Florida waters as identified by DNA barcoding.

DNA barcoding was used to identify prey fragments recovered from the stomachs of lionfish harvested during the 2016 Sarasota Lionfish Derby. A total of 305 prey fragments were recovered from 50 stomachs (mean = 4.6 per stomach), of which 184 (60.3%) fragments could be identified to either species or genus when Cytochrome Oxidase I (COI) sequences were queried against the Barcode of Life Database. We identified 21 fish prey species which represented fourteen families and accounted for 95.7% of genetically identifiable prey items. The remaining prey items identified corresponded to six crustacean species. The four most common prey taxa in lionfish stomachs were Ptereleotris calliura (24.3%), an unidentified Microgobius species (20.4%), Diplectum formosum (14.3%), and Apogon aurolineatus (12.2%). The most frequently observed crustacean species, Metapenaeopsis goodei, was found in only three stomachs (6.1%). We also report eleven taxa as putative novel lionfish prey species, most of which are common in Florida waters. Sixteen prey items were identified as lionfish (P. volitans); however, it was not definitive whether these detections were due to cross contamination or cannibalization. This represents the first report of lionfish diets from Florida waters in the Eastern Gulf of Mexico based on barcoding efforts. Our results are largely congruent with previous COI barcoding based studies of lionfish diets, indicating these predators to be generalists exhibiting preferences for specific prey traits but with regional differences in their diets.

Molecular taxonomy of endemic coastal Ligia isopods from the Hawaiian Islands: re-description of L. hawaiensis and description of seven novel cryptic species.

Past phylogeographic work has shown Ligia hawaiensis, a coastal isopod species endemic to the Hawaiian Islands, to be a paraphyletic complex of several highly genetically divergent yet morphologically cryptic lineages. Despite the need for a taxonomic revision of this species, the lack of morphological differentiation has proven an impediment to formally describe new Ligia species in the region. Molecular characters and species delimitation approaches have been successfully used to formally describe cryptic species in other crustacean taxa, suggesting they may aid taxonomic revisions of L. hawaiensis. Herein, various distance- and tree-based molecular species delimitation approaches are applied on a concatenated dataset comprised of both mitochondrial and nuclear gene sequences of L. hawaiensis and L. perkinsi, a terrestrial species endemic to the Hawaiian archipelago. Results of these analyses informed a taxonomic revision leading to the redescription of L. hawaiensis and the description of seven new cryptic species on the basis of molecular characters: L. dante, L. eleluensis, L. honu, L. kamehameha, L. mauinuiensis, L. pele, and L. rolliensis. These coastal Ligia species from the Hawaiian archipelago appear to be largely limited to single islands, where they appear largely constrained to volcanic rift zones suggesting allopatric events at local scales may drive diversification for poorly dispersing organisms in the Hawaiian coastlines. Additional work remains needed to fully assess the role of said events; however, the description of these novel species underscore their potential to aid in studies of local diversification of marine organisms in Hawai'i. Lastly, this represents the first application of molecular taxonomic approaches to formally describe genetic lineages found in Ligia isopods as species, underscoring the promise these methods hold to taxonomic revisions in other species in the genus shown to harbor cryptic genetic lineages.

Molecular approaches uncover cryptic diversity in intertidal Ligia isopods (Crustacea, Isopoda, Ligiidae) across the southern Africa coastline.

Recent phylogeographic studies along the coastline of southern Africa have uncovered cryptic diversity in several coastal invertebrates, including direct developing crustaceans in the superorder Peracarida. These findings indicating the possible existence of additional cryptic diversity in other yet to be studied peracarids, particularly those known to harbor said cryptic diversity in other regions of the world. Isopods in the genus Ligia are one such taxon. They inhabit patchy rocky beaches, are direct developers, avoid the open water, and exhibit other biological traits that severely constrain their dispersal potential (e.g., poor desiccation resistance). These traits are thought to have led to long-term isolation of populations, and allopatric diversification in Ligia species around the world; however, Ligia species in southern Africa, where three endemic Ligia species of uncertain validity are known to exist, remain unstudied to date. In this study, we used mitochondrial and nuclear markers to characterize Ligia collected in 18 localities from Namibia to the KwaZulu-Natal region of South Africa. We report the presence of cryptic lineages within Ligia species in the region that suggest the need for taxonomic reevaluation of these isopod species.

Out of Asia: mitochondrial evolutionary history of the globally introduced supralittoral isopod Ligia exotica.

The native ranges and invasion histories of many marine species remain elusive due to a dynamic dispersal process via marine vessels. Molecular markers can aid in identification of native ranges and elucidation of the introduction and establishment process. The supralittoral isopod Ligia exotica has a wide tropical and subtropical distribution, frequently found in harbors and ports around the globe. This isopod is hypothesized to have an Old World origin, from where it was unintentionally introduced to other regions via wooden ships and solid ballast. Its native range, however, remains uncertain. Recent molecular studies uncovered the presence of two highly divergent lineages of L. exotica in East Asia, and suggest this region is a source of nonindigenous populations. In this study, we conducted phylogenetic analyses (Maximum Likelihood and Bayesian) of a fragment of the mitochondrial 16S ribosomal (r)DNA gene using a dataset of this isopod that greatly expanded previous representation from Asia and putative nonindigenous populations around the world. For a subset of samples, sequences of 12S rDNA and NaK were also obtained and analyzed together with 16S rDNA. Our results show that L. exotica is comprised of several highly divergent genetic lineages, which probably represent different species. Most of the 16S rDNA genetic diversity (48 haplotypes) was detected in East and Southeast Asia. Only seven haplotypes were observed outside this region (in the Americas, Hawai'i, Africa and India), which were identical or closely related to haplotypes found in East and Southeast Asia. Phylogenetic patterns indicate the L. exotica clade originated and diversified in East and Southeast Asia, and only members of one of the divergent lineages have spread out of this region, recently, suggesting the potential to become invasive is phylogenetically constrained.

Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods.

Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 115 islands of different ages and geological origins spread across the western Indian Ocean. They are well known for their rich biodiversity with recent reports of cryptic species in terrestrial Seychellois organisms. Despite these studies, it is unclear whether coastal invertebrates from the Seychelles harbor any cryptic diversity. In this study, we examined patterns of genetic diversity and isolation within Ligia isopods across the Seychelles archipelago by characterizing individuals from locations across both inner and outer islands of the Seychelles using mitochondrial and nuclear markers. We report the presence of highly divergent lineages of independent origin. At Aldabra Atoll, we uncovered a lineage closely related to the Ligia vitiensis cryptic species complex. Within the inner islands of Cousine, Silhouette, and Mahé we detected the presence of two moderately divergent and geographically disjunct lineages most closely related to Ligia dentipes. Our findings suggest that the Seychelles may harbor at least three novel species of Ligia in need of description and that these species may have originated independently.

First record of the Ligia baudiniana species complex in the American Gulf of Mexico Coastline, as confirmed by morphological and molecular approaches.

Ligia isopods exhibit a constrained morphology that makes identification difficult. In the Greater Caribbean, a convoluted taxonomic history has left the distributional limits of Ligia baudiniana unclear. To date, no confirmed records of this species exist from the American Gulf of Mexico. Herein, we report the presence of L. baudiniana in Sarasota-Manatee Florida, as confirmed by morphological and molecular approaches. This is the first record of this species in the region and a ~300Km extension of its range. Specimens were collected in mangroves, underscoring the importance of protecting these habitats.

Constrained body shape among highly genetically divergent allopatric lineages of the supralittoral isopod Ligia occidentalis (Oniscidea).

Multiple highly divergent lineages have been identified within Ligia occidentalis sensu lato, a rocky supralittoral isopod distributed along a ~3000 km latitudinal gradient that encompasses several proposed marine biogeographic provinces and ecoregions in the eastern Pacific. Highly divergent lineages have nonoverlapping geographic distributions, with distributional limits that generally correspond with sharp environmental changes. Crossbreeding experiments suggest postmating reproductive barriers exist among some of them, and surveys of mitochondrial and nuclear gene markers do not show evidence of hybridization. Populations are highly isolated, some of which appear to be very small; thus, the effects of drift are expected to reduce the efficiency of selection. Large genetic divergences among lineages, marked environmental differences in their ranges, reproductive isolation, and/or high isolation of populations may have resulted in morphological differences in L. occidentalis, not detected yet by traditional taxonomy. We used landmark-based geometric morphometric analyses to test for differences in body shape among highly divergent lineages of L. occidentalis, and among populations within these lineages. We analyzed a total of 492 individuals from 53 coastal localities from the southern California Bight to Central Mexico, including the Gulf of California. We conducted discriminant function analyses (DFAs) on body shape morphometrics to assess morphological variation among genetically differentiated lineages and their populations. We also tested for associations between phylogeny and morphological variation, and whether genetic divergence is correlated to multivariate morphological divergence. We detected significant differences in body shape among highly divergent lineages, and among populations within these lineages. Nonetheless, neither lineages nor populations can be discriminated on the basis of body shape, because correct classification rates of cross-validated DFAs were low. Genetic distance and phylogeny had weak to no effect on body shape variation. The supralittoral environment appears to exert strong stabilizing selection and/or strong functional constraints on body shape in L. occidentalis, thereby leading to morphological stasis in this isopod.

A complex evolutionary history in a remote archipelago: phylogeography and morphometrics of the Hawaiian endemic Ligia isopods.

Compared to the striking diversification and levels of endemism observed in many terrestrial groups within the Hawaiian Archipelago, marine invertebrates exhibit remarkably lower rates of endemism and diversification. Supralittoral invertebrates restricted to specific coastal patchy habitats, however, have the potential for high levels of allopatric diversification. This is the case of Ligia isopods endemic to the Hawaiian Archipelago, which most likely arose from a rocky supralittoral ancestor that colonized the archipelago via rafting, and diversified into rocky supralittoral and inland lineages. A previous study on populations of this isopod from O'ahu and Kaua'i revealed high levels of allopatric differentiation, and suggested inter-island historical dispersal events have been rare. To gain a better understanding on the diversity and evolution of this group, we expanded prior phylogeographic work by incorporating populations from unsampled main Hawaiian Islands (Maui, Moloka'i, Lana'i, and Hawai'i), increasing the number of gene markers (four mitochondrial and two nuclear genes), and conducting Maximum likelihood and Bayesian phylogenetic analyses. Our study revealed new lineages and expanded the distribution range of several lineages. The phylogeographic patterns of Ligia in the study area are complex, with Hawai'i, O'ahu, and the Maui-Nui islands sharing major lineages, implying multiple inter-island historical dispersal events. In contrast, the oldest and most geographically distant of the major islands (Kaua'i) shares no lineages with the other islands. Our results did not support the monophyly of all the supralittoral lineages (currently grouped into L. hawaiensis), or the monophyly of the terrestrial lineages (currently grouped into L. perkinsi), implying more than one evolutionary transition between coastal and inland forms. Geometric-morphometric analyses of three supralittoral clades revealed significant body shape differences among them. A taxonomic revision of Hawaiian Ligia is warranted. Our results are relevant for the protection of biodiversity found in an environment subject to high pressure from disturbances.

Molecular systematics of the deep-sea hydrothermal vent endemic Brachyuran family Bythograeidae: a comparison of three Bayesian species tree methods.

Brachyuran crabs of the family Bythograeidae are endemic to deep-sea hydrothermal vents and represent one of the most successful groups of macroinvertebrates that have colonized this extreme environment. Occurring worldwide, the family includes six genera (Allograea, Austinograea, Bythograea, Cyanagraea, Gandalfus, and Segonzacia) and fourteen formally described species. To investigate their evolutionary relationships, we conducted Maximum Likelihood and Bayesian molecular phylogenetic analyses, based on DNA sequences from fragments of three mitochondrial genes (16S rDNA, Cytochrome oxidase I, and Cytochrome b) and three nuclear genes (28S rDNA, the sodium-potassium ATPase a-subunit 'NaK', and Histone H3A). We employed traditional concatenated (i.e., supermatrix) phylogenetic methods, as well as three recently developed Bayesian multilocus methods aimed at inferring species trees from potentially discordant gene trees. We found strong support for two main clades within Bythograeidae: one comprising the members of the genus Bythograea; and the other comprising the remaining genera. Relationships within each of these two clades were partially resolved. We compare our results with an earlier hypothesis on the phylogenetic relationships among bythograeid genera based on morphology. We also discuss the biogeography of the family in the light of our results. Our species tree analyses reveal differences in how each of the three methods weighs conflicting phylogenetic signal from different gene partitions and how limits on the number of outgroup taxa may affect the results.

Phylogeography of supralittoral rocky intertidal Ligia isopods in the pacific region from central California to central Mexico.

BACKGROUND: Ligia isopods are widely distributed in the Pacific rocky intertidal shores from central California to central Mexico, including the Gulf of California. Yet, their biological characteristics restrict them to complete their life cycles in a very narrow range of the rocky intertidal supralittoral. Herein, we examine phylogeographic patterns of Ligia isopods from 122 localities between central California and central Mexico. We expect to find high levels of allopatric diversity. In addition, we expect the phylogeographic patterns to show signatures of past vicariant events that occurred in this geologically dynamic region. METHODOLOGY/PRINCIPAL FINDINGS: We sequenced two mitochondrial genes (Cytochrome Oxidase I and 16S ribosomal DNA). We conducted Maximum Likelihood and Bayesian phylogenetic analyses. We found many divergent clades that, in general, group according to geography. Some of the most striking features of the Ligia phylogeographic pattern include: (1) deep mid-peninsular phylogeographic breaks on the Pacific and Gulf sides of Baja peninsula; (2) within the Gulf lineages, the northern peninsula is most closely related to the northern mainland, while the southern peninsula is most closely related to the central-southern mainland; and, (3) the southernmost portion of the peninsula (Cape Region) is most closely related to the southernmost portion of mainland. CONCLUSIONS/SIGNIFICANCE: Our results shed light on the phylogenetic relationships of Ligia populations in the study area. This study probably represents the finest-scale phylogeographic examination for any organism to date in this region. Presence of highly divergent lineages suggests multiple Ligia species exist in this region. The phylogeographic patterns of Ligia in the Gulf of California and Baja peninsula are incongruent with a widely accepted vicariant scenario among phylogeographers, but consistent with aspects of alternative geological hypotheses and phylo- and biogeographic patterns of several other taxa. Our findings contribute to the ongoing debate regarding the geological origin of this important biogeographic region.