Comparative Mitogenomics in Hyalella (Amphipoda: Crustacea).

We present the sequencing and comparative analysis of 17 mitochondrial genomes of Nearctic and Neotropical amphipods of the genus Hyalella, most from the Andean Altiplano. The mitogenomes obtained comprised the usual 37 gene-set of the metazoan mitochondrial genome showing a gene rearrangement (a reverse transposition and a reversal) between the North and South American Hyalella mitogenomes. Hyalella mitochondrial genomes show the typical AT-richness and strong nucleotide bias among codon sites and strands of pancrustaceans. Protein-coding sequences are biased towards AT-rich codons, with a preference for leucine and serine amino acids. Numerous base changes (539) were found in tRNA stems, with 103 classified as fully compensatory, 253 hemi-compensatory and the remaining base mismatches and indels. Most compensatory Watson-Crick switches were AU -> GC linked in the same haplotype, whereas most hemi-compensatory changes resulted in wobble GU and a few AC pairs. These results suggest a pairing fitness increase in tRNAs after crossing low fitness valleys. Branch-site level models detected positive selection for several amino acid positions in up to eight mitochondrial genes, with atp6 and nad5 as the genes displaying more sites under selection.

Phylogenomics of the Hyalella amphipod species-flock of the Andean Altiplano.

Species diversification in ancient lakes has enabled essential insights into evolutionary theory as they embody an evolutionary microcosm compared to continental terrestrial habitats. We have studied the high-altitude amphipods of the Andes Altiplano using mitogenomic, nuclear ribosomal and single-copy nuclear gene sequences obtained from 36 Hyalella genomic libraries, focusing on species of the Lake Titicaca and other water bodies of the Altiplano northern plateau. Results show that early Miocene South American lineages have recently (late Pliocene or early Pleistocene) diversified in the Andes with a striking morphological convergence among lineages. This pattern is consistent with the ecological opportunities (access to unoccupied resources, initial relaxed selection on ecologically-significant traits and low competition) offered by the lacustrine habitats established after the Andean uplift.

The age and diversification of metacrangonyctid subterranean amphipod crustaceans revisited.

The Metacrangonyctidae are a small family of amphipod crustaceans of marine origin found only in subterranean continental waters. They display a broad but punctuated distribution between the Caribbean and the Arabian Peninsula, with major disjunctions either due to vicariance by plate tectonics or to occurrence of recent episodes of long-distance transoceanic dispersal. We re-examine the phylogeny of the family and the time frame for its diversification using mitochondrial genomes in the light of two key taxa recently discovered, from Oman (Arabian Peninsula) and the Rif area of Morocco, respectively. We also use a novel fossil calibration scheme of the mitogenome phylogeny. Results of previous analyses based on palaeogeographic calibrations are not contradicted by the new approach, with vicariance by plate tectonics remaining as the main explanatory factor for the amphi-Atlantic distribution displayed by this ancient group of subterranean amphipods.

Two new species of Pseudoniphargus (Amphipoda: Pseudoniphargidae) from southern Spain.

Two new species of subterranean water amphipod crustaceans of the genus Pseudoniphargus (Pseudoniphargidae) are described from gypsum caves of Andalusia, southern Spain. Both species share the extreme elongation of the male third uropod, a striking feature frequently reported in the genus and that seems to have arisen independently in several lineages. These findings raise the number of species of Pseudoniphargus known from the area to 17.

Species delimitation and mitogenome phylogenetics in the subterranean genus Pseudoniphargus (Crustacea: Amphipoda).

The amphi-Atlantic distributions exhibited by many thalassoid stygobiont (obligate subterranean) crustaceans have been explained by fragmentation by plate tectonics of ancestral shallow water marine populations. The amphipod stygobiont genus Pseudoniphargus is distributed across the Mediterranean region but also in the North Atlantic archipelagos of Bermuda, Azores, Madeira and the Canaries. We used species delimitation methods and mitogenome phylogenetic analyses to clarify the species diversity and evolutionary relationships within the genus and timing their diversification. Analyses included samples from the Iberian Peninsula, northern Morocco, the Balearic, Canarian, Azores and Madeira archipelagoes plus Bermuda. In most instances, morphological and molecular-based species delimitation analyses yielded consistent results. Notwithstanding, in a few cases either incipient speciation with no involvement of detectable morphological divergence or species crypticism were the most plausible explanations for the disagreement found between morphological and molecular species delimitations. Phylogenetic analyses based on a robust calibrated mitochondrial tree suggested that Pseudoniphargus lineages have a younger age than for other thalassoid amphipods displaying a disjunct distribution embracing both sides of the Atlantic Ocean. A major split within the family was estimated to occur at the Paleocene, when a lineage from Northern Iberian Peninsula diverged from the rest of pseudoniphargids. Species diversification in the peri-Mediterranean area was deduced to occur in early Miocene to Tortonian times, while in the Atlantic islands it started in the Pliocene. Our results show that the current distribution pattern of Pseudoniphargus resulted from a complex admix of relatively ancient vicariance events and several episodes of long- distance dispersal.

A new species of Hyalella from the High Andes of Ecuador (Crustacea, Amphipoda, Hyalellidae).

Hyalella cajasisp. n. is described from high altitude shallow water lakes in southern Ecuador. This is the second representative of the genus recorded in the country after H. meinerti. The new species shares with nine South American species of the genus the display of a smooth, non-processiferous body, a male first uropod with a modified curved robust seta on the endopod, and six pairs of sternal gills. The new taxon can be distinguished from these species based on the presence/absence of eyes; relative length of antenna 1 with respect to antenna 2; presence/absence of short pointed robust seta distally on palp of maxilla 1; number of pappose setae proximally on medial margin of inner lobe of maxilla 2; elongation and curvature of the modified robust seta of endopod of male uropod 1; relative length of ramus of uropod 3 with respect to protopod; and armature and outline of telson, among other features. It seems to be a high-altitude endemic to the Cajas Massif in Azuay Province, being replaced in the same area at lower altitudes by H. meinerti.

A new species of Notodiaptomus from the Ecuadorian Andes (Copepoda, Calanoida, Diaptomidae).

Notodiaptomus cannarensissp. n. is described from a reservoir on the Amazonian slope of the Ecuadorian Andes. The new species is unique among diaptomid calanoid copepods in the display of hypertrophied, symmetrical wing-like extensions at each side of the female composite genital somite. Furthermore, it displays a female urosome reduced to only two somites due to the incorporation of abdominal somites III and IV to the composite genital double-somite, and a male right fifth leg with the outer spine of second exopodal segment recurved and implanted proximally on margin. It differs from any other Notodiaptomus in the display of a large rectangular lamella on proximal segment of exopod of male right fifth leg. The species is currently known only from Mazar reservoir, a eutrophic water body placed above 2127 m a.s.l. on the River Paute (Cañar Province; southern Ecuador), where it is the most common crustacean in the water column.

Phylogenetic evidence that both ancient vicariance and dispersal have contributed to the biogeographic patterns of anchialine cave shrimps.

Cave shrimps from the genera Typhlatya, Stygiocaris and Typhlopatsa (Atyidae) are restricted to specialised coastal subterranean habitats or nearby freshwaters and have a highly disconnected distribution (Eastern Pacific, Caribbean, Atlantic, Mediterranean, Madagascar, Australia). The combination of a wide distribution and a limited dispersal potential suggests a large-scale process has generated this geographic pattern. Tectonic plates that fragment ancestral ranges (vicariance) has often been assumed to cause this process, with the biota as passive passengers on continental blocks. The ancestors of these cave shrimps are believed to have inhabited the ancient Tethys Sea, with three particular geological events hypothesised to have led to their isolation and divergence; (1) the opening of the Atlantic Ocean, (2) the breakup of Gondwana, and (3) the closure of the Tethys Seaway. We test the relative contribution of vicariance and dispersal in the evolutionary history of this group using mitochondrial genomes to reconstruct phylogenetic and biogeographic scenarios with fossil-based calibrations. Given that the Australia/Madagascar shrimp divergence postdates the Gondwanan breakup, our results suggest both vicariance (the Atlantic opening) and dispersal. The Tethys closure appears not to have been influential, however we hypothesise that changing marine currents had an important early influence on their biogeography.

Mitochondrial genome rearrangements at low taxonomic levels: three distinct mitogenome gene orders in the genus Pseudoniphargus (Crustacea: Amphipoda).

A comparison of mitochondrial genomes of three species of the amphipod Pseudoniphargus revealed the occurrence of a surprisingly high level of gene rearrangement involving protein-coding genes that is a rare phenomenon at low taxonomic levels. The three Pseudoniphargus mitogenomes also display a unique gene arrangement with respect to either the presumed Pancrustacean order or those known for other amphipods. Relative long non-coding sequences appear adjacent to the putative breakage points involved in gene rearrangements of protein coding genes. Other details of the newly obtained mitochondrial genomes - e.g., gene content, nucleotide composition and codon usage - are similar to those found in the mitogenomes of other amphipod species studied. They all contain the typical mitochondrial genome set consisting of 13 protein-coding genes, 22 tRNAs, and two rRNAS, as well as a large control region. The secondary structures and characteristics of tRNA and ribosomal mitochondrial genes of these three species are also discussed.

The mitogenome of the amphipod Hyalella lucifugax (Crustacea) and its phylogenetic placement.

The mitogenome of Hyalella lucifugax from Lake Titicaca, obtained using Illumina NGS technology, is described. The mitogenome attains 14,994 bp (although the control region could not be completed) and comprises the standard set of 2 rRNAs, 13 protein-coding genes, and 22 tRNA genes, plus two non-coding regions. A phylogenetic analysis based on the protein-coding mitochondrial genes from representatives from all amphipod genera with available sequences in GenBank recovers the monophyly of H. lucifugax with the superfamily Talitroidea.

The complete mitochondrial genome of the cave shrimp Typhlatya miravetensis (Decapoda, Atyidae) and its systematic position.

The complete mitochondrial genome of Typhlatya miravetensis from one of its only three known localities (Ullal de la Rabla de Miravet, Castellón, Spain) is presented here. The mitogenome is 15,865 bp in length and includes the standard set of two rRNAs, two non-coding regions plus 13 protein-coding genes. The later have been used to perform a phylogenetic analysis together with other Caridea representatives with mitogenome data in GenBank, inferring a close relationship with the Hawaiian volcano shirmp (Halocaridina rubra) within the family Atyidae.

Ingolfiellamaldivensis sp. n. (Crustacea, Amphipoda, Ingolfiellidae) from coral reef sand off Magoodhoo island, Maldives.

A new species of marine interstitial wormshrimp, Ingolfiellamaldivensis, is described from coral sand on the inner and outer reef off Magoodhoo island, Faafu atoll, Maldives. Six females were found and compared to other species from the Maldives and those bordering the Indian Ocean and beyond. Morphological resemblance ties it to a species from the Caribbean island of Curaçao. Both species are found in shallow sublittoral interstitial spaces.

Next-generation sequencing, phylogenetic signal and comparative mitogenomic analyses in Metacrangonyctidae (Amphipoda: Crustacea).

BACKGROUND: Comparative mitochondrial genomic analyses are rare among crustaceans below the family or genus level. The obliged subterranean crustacean amphipods of the family Metacrangonyctidae, found from the Hispaniola (Antilles) to the Middle East, including the Canary Islands and the peri-Mediterranean region, have an evolutionary history and peculiar biogeography that can respond to Tethyan vicariance. Indeed, recent phylogenetic analysis using all protein-coding mitochondrial sequences and one nuclear ribosomal gene have lent support to this hypothesis (Bauzà-Ribot et al. 2012). RESULTS: We present the analyses of mitochondrial genome sequences of 21 metacrangonyctids in the genera Metacrangonyx and Longipodacrangonyx, covering the entire geographical range of the family. Most mitogenomes were attained by next-generation sequencing techniques using long-PCR fragments sequenced by Roche FLX/454 or GS Junior pyro-sequencing, obtaining a coverage depth per nucleotide of up to 281×. All mitogenomes were AT-rich and included the usual 37 genes of the metazoan mitochondrial genome, but showed a unique derived gene order not matched in any other amphipod mitogenome. We compare and discuss features such as strand bias, phylogenetic informativeness, non-synonymous/synonymous substitution rates and other mitogenomic characteristics, including ribosomal and transfer RNAs annotation and structure. CONCLUSIONS: Next-generation sequencing of pooled long-PCR amplicons can help to rapidly generate mitogenomic information of a high number of related species to be used in phylogenetic and genomic evolutionary studies. The mitogenomes of the Metacrangonyctidae have the usual characteristics of the metazoan mitogenomes (circular molecules of 15,000-16,000 bp, coding for 13 protein genes, 22 tRNAs and two ribosomal genes) and show a conserved gene order with several rearrangements with respect to the presumed Pancrustacean ground pattern. Strand nucleotide bias appears to be reversed with respect to the condition displayed in the majority of crustacean mitogenomes since metacrangonyctids show a GC-skew at the (+) and (-) strands; this feature has been reported also in the few mitogenomes of Isopoda (Peracarida) known thus far. The features of the rRNAs, tRNAs and sequence motifs of the control region of the Metacrangonyctidae are similar to those of the few crustaceans studied at present.

A new genus of speleophriid copepod (Copepoda: Misophrioida) from a cenote in the Yucatan, Mexico with a phylogenetic analysis at the species level.

A new genus and species of speleophriid copepod, Mexicophria cenoticola gen. et sp. nov., is described based on material collected from a cenote in the Yucatan Peninsula of Mexico. It is characterised by relatively reduced fifth legs that are located adjacent to the ventral midline in both sexes, by the possession of a bulbous swelling on the first antennulary segment in both sexes, and by the reduced setation of the swimming legs. The presence of just one inner margin seta on the second endopodal segment of legs 2 to 4 is a unique feature for the family. A phylogenetic analysis places the new genus on a basal lineage of the family together with its sister taxon, Boxshallia Huys, 1988, from Lanzarote in the Canary Islands, and recovers the existing genera as monophyletic units. The zoogeography is discussed at local, regional, ocean basin  and global scales.

A new Psammogammarus (Amphipoda: Eriopisidae) from anchialine pools on the Exuma Cays, Bahamas.

Psammogammarus lucayensis sp. nov. is described from anchialine pools on Little Iguana Cay (Exuma Cays, Great Bahama Bank). It can be easily distinguished from the other 14 members of the genus by the combination of: 1) carpus of G2 longer than broad; 2) male G2 palm margin non-excavated, evenly convex and devoid of strong mid-palmar robust setae; 3) basis of P7 with subparallel margins; 4) armature arrangement of ventral margin of epimeral plates as 0-2-3; 5) posteroventral angle of epimeral plate III strongly produced; 6) protopod of U2 with distomedial angle armed with comb of 3-4 robust setae; 7) U3 endopod as long as exp1; and 8) telson with robust setae on tip. The generic diagnosis is amended in order to allow the precise characterization of members of Psammogammarus compared to other eriopisids.

Mitogenomic phylogenetic analysis supports continental-scale vicariance in subterranean thalassoid crustaceans.

Many continental subterranean water crustaceans ("stygobionts") display extreme disjunct distributions, where different species in the same genus are isolated on continents or islands separated by broad oceanic expanses. Despite their freshwater habitat, most of these taxa appear to be most closely related to typical marine groups ("thalassoid" origin). Among the hadzioids-thalassoid amphipods including the stygobiont families Hadziidae, Pseudoniphargidae, and Metacrangonyctidae-several genera are restricted to inland groundwaters ranging from the Caribbean region to the Mediterranean and Middle East, including interspersed oceanic islands. This distribution might have arisen from Tethyan vicariance triggered by the sequential occlusion of the former Tethys Sea, a vast circumtropical ocean existing from the Middle Jurassic up to 20 million years ago (mya). Previous studies have been based on morphological analyses or limited DNA sequence data, making it difficult to test this hypothesis. We used complete mitochondrial protein-coding gene sequences, mainly obtained by next-generation sequencing methods and a nuclear ribosomal gene to resolve the phylogeny and to establish a time frame for diversification of the family Metacrangonyctidae (Amphipoda). The results were consistent with the plate tectonics vicariance hypothesis, with major diversifications occurring between 96 and 83 mya.

A new marine interstitial Psammogammarus (Crustacea, Amphipoda, Melitidae) from Gura Ici Island, off western Halmahera (North Moluccas, Indonesia), and an overview of the genus.

Psammogammarus wallaceisp. n. is described from the shallow marine interstitial of a sand and coral rubble beach on the Gura Ici islands (North Moluccas; Indonesia). This is the first record of this circum-tropical genus from SE Asia, with the geographically closest relative inhabiting the Ryukyu archipelago in Japan. The new species is highly distinctive by the display of sexual dimorphism on pleopod II, with the medial margin of the male proximal article of exopod provided with a comb of short, blunt curved spinules; no other representative of the genus is known to display sexually-dimorphic appendages aside of the gnathopods. The new species is also noteworthy by the outline of the palm margin of male gnathopod II, hardly excavated, and by showing a carpus broader than long. An overview of the genus Psammogammarus with 14 species to date is provided.

Islands beneath islands: phylogeography of a groundwater amphipod crustacean in the Balearic archipelago.

BACKGROUND: Metacrangonyctidae (Amphipoda, Crustacea) is an enigmatic continental subterranean water family of marine origin (thalassoid). One of the species in the genus, Metacrangonyx longipes, is endemic to the Balearic islands of Mallorca and Menorca (W Mediterranean). It has been suggested that the origin and distribution of thalassoid crustaceans could be explained by one of two alternative hypotheses: (1) active colonization of inland freshwater aquifers by a marine ancestor, followed by an adaptative shift; or (2) passive colonization by stranding of ancestral marine populations in coastal aquifers during marine regressions. A comparison of phylogenies, phylogeographic patterns and age estimations of clades should discriminate in favour of one of these two proposals. RESULTS: Phylogenetic relationships within M. longipes based on three mitochondrial DNA (mtDNA) and one nuclear marker revealed five genetically divergent and geographically structured clades. Analyses of cytochrome oxidase subunit 1 (cox1) mtDNA data showed the occurrence of a high geographic population subdivision in both islands, with current gene flow occurring exclusively between sites located in close proximity. Molecular-clock estimations dated the origin of M. longipes previous to about 6 Ma, whereas major cladogenetic events within the species took place between 4.2 and 2.0 Ma. CONCLUSIONS: M. longipes displayed a surprisingly old and highly fragmented population structure, with major episodes of cladogenesis within the species roughly correlating with some of the major marine transgression-regression episodes that affected the region during the last 6 Ma. Eustatic changes (vicariant events) -not active range expansion of marine littoral ancestors colonizing desalinated habitats-explain the phylogeographic pattern observed in M. longipes.

Evolution in caves: Darwin's 'wrecks of ancient life' in the molecular era.

Cave animals have historically attracted the attention of evolutionary biologists because of their bizarre 'regressive' characters and convergent evolution. However, understanding of their biogeographic and evolutionary history, including mechanisms of speciation, has remained elusive. In the last decade, molecular data have been obtained for subterranean taxa and their surface relatives, which have allowed some of the classical debates on the evolution of cave fauna to be revisited. Here, we review some of the major studies, focusing on the contribution of phylogeography in the following areas: biogeographic history and the relative roles of dispersal and vicariance, colonization history, cryptic species diversity and modes of speciation of cave animals. We further consider the limitations of current research and prospects for the future. Phylogeographic studies have confirmed that cave species are often cryptic, with highly restricted distributions, but have also shown that their divergence and potential speciation may occur despite the presence of gene flow from surface populations. Significantly, phylogeographic studies have provided evidence for speciation and adaptive evolution within the confines of cave environments, questioning the assumption that cave species evolved directly from surface ancestors. Recent technical developments involving 'next generation' DNA sequencing and theoretical developments in coalescent and population modelling are likely to revolutionize the field further, particularly in the study of speciation and the genetic basis of adaptation and convergent evolution within subterranean habitats. In summary, phylogeographic studies have provided an unprecedented insight into the evolution of these unique fauna, and the future of the field should be inspiring and data rich.