Phylogeny, molecular ecology and taxonomy of southern Iberian lineages of Triops mauritanicus (Crustacea: Notostraca)

Mapping the Geographic Distribution of Large Branchiopods in Algeria and a checklist update

The objective of this study was to assess the diversity and distribution of large branchiopods in the Algerian Sahara and Hauts Plateaux. The survey identified a total of eleven species, classified into seven Anostraca, two Notostraca, and two Spinicaudata. Large branchiopods were found in 76.6% of the sites surveyed. In particular, new records of Triops granarius (Lucas, 1864) were obtained from the Tasilli NAjjer region (Central Sahara), while Eocyzicus saharicus (Gauthier, 1937) was added to the list of large branchiopods of Algeria, bringing the total number of species in Algeria to twenty-four. In addition, this study examines the latitudinal gradient of major branchiopod assemblages in Algeria, extending from the northern Mediterranean coast to the arid regions of the Sahara. The study identifies eight major assemblages of large branchiopods distributed across different ecoclimatic zones that occur along the latitudinal and longitudinal axes of the country. In addition, the study draws parallels between Algerian assemblages and those in neighboring Morocco and Tunisia.

Pleistocene allopatric differentiation followed by recent range expansion explains the distribution and molecular diversity of two congeneric crustacean species in the Palaearctic

Pleistocene glaciations had a tremendous impact on the biota across the Palaearctic, resulting in strong phylogeographic signals of range contraction and rapid postglacial recolonization of the deglaciated areas. Here, we explore the diversity patterns and history of two sibling species of passively dispersing taxa typical of temporary ponds, fairy shrimps (Anostraca). We combine mitochondrial (COI) and nuclear (ITS2 and 18S) markers to conduct a range-wide phylogeographic study including 56 populations of Branchinecta ferox and Branchinecta orientalis in the Palaearctic. Specifically, we investigate whether their largely overlapping ranges in Europe resulted from allopatric differentiation in separate glacial refugia followed by a secondary contact and reconstruct their postglacial recolonization from the inhabited refugia. Our results suggest the existence of distinct refugia for the two species, with genetic divergence among intraspecific lineages consistent with late Pleistocene glacial cycles. While B. ferox lineages originated from Mediterranean refugia, the origin of B. orientalis lineages was possibly located on the Pannonian Plain. We showed that most dispersal events predominantly happened within 100 km, coupled with several recent long-distance events (> 1000 km). Hence the regional habitat density of suitable habitats in Central Europe is possibly a key to the co-existence of the two species. Overall, our study illustrates how isolation in combination with stochastic effects linked to glacial periods are important drivers of the allopatric differentiation of Palaearctic taxa.

Limited long-distance dispersal success in a Western European fairy shrimp evidenced by nuclear and mitochondrial lineage structuring

Anostraca are known by their ability for long-distance dispersal, but the existence in several species of deep, geographically structured mtDNA lineages suggests their populations are subjected to allopatric differentiation, isolation, and prevalence of local scale dispersion. Tanymastix stagnalis is one of the most widespread species of Anostraca and previous studies revealed an unclear geographical pattern of mtDNA genetic diversity. Here, we analyze populations from the Iberian and Italian Peninsulas, Central Europe, and Scandinavia, with the aim to characterize the patterns of genetic diversity in a spatio-temporal framework using mtDNA and nuclear markers to test gene flow among close populations. For these aims we built a time-calibrated phylogeny and carried out Bayesian phylogeographic analyses using a continuous diffusion model. Our results indicated that T. stagnalis presents a deeply structured genetic diversity, including 7 ancient lineages, some of them even predating the Pleistocene. The Iberian Peninsula harbors high diversity of lineages, with strong isolation and recent absence of gene flow between populations. Dispersal at local scale seems to be the prevailing dispersal mode of T. stagnalis, which exhibits a pattern of isolation-by-distance in the Iberian Peninsula. We remark the vulnerability of most of these lineages, given the limited known geographic distribution of some of them, and the high risk of losing important evolutionary potential for the species.

Characterization of the complete mitochondrial genome of Chinese Triops granarius and implications for species delimitation

The mt genome of T. granarius (15.121 bp), containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and one control region, present the typical pattern of phyllopod mt genomes from the perspective of gene content and order. All PCGs initiate with standard start codon of ATN and share the complete stop codon of TAA or TAG, whereas nd1 initiates with GTG, nd2 terminates with AGA and nd4 terminates with a single T. The secondary structures of rrnL and rrnS comprise of 48 helices and 32 helices, respectively. The patterns of evolutionary rate heterogeneity were observed at different levels in Triops. Phylogenetic analyses were performed based on the nucleotide sequences and amino acid sequences showed that Asian T. granarius was a sister group to (T. longicaudatus + T. australiensis), and T. cancriformis was the basal clade of Triops. Furthermore, we investigated the genetic diversity and phylogenetic relationships of different T. granarius s.l. populations. Ten phylogenetic lineages are separated on species level by mean maximum likelihood distance ≥ 12.2% in the cox1 gene. While the six populations occurring in Inner Mongolia of China, Mongolia and Russia, investigated for haplotypes belonged to the same haplotype networks.

Discriminating between the effects of founding events and reproductive mode on the genetic structure of Triops populations (Branchiopoda: Notostraca)

Crustaceans that initially colonize a freshwater temporary pond can strongly bias the subsequent genetic composition of the population, causing nearby populations to be genetically distinct. In addition, these crustaceans have various reproductive modes that can influence genetic differentiation and diversity within and between populations. We report on two species of tadpole shrimp, Triops newberryi and Triops longicaudatus "short", with different reproductive modes. Reproduction in the tadpole shrimp can occur clonally (parthenogenesis), with self fertilization (hermaphroditism), or through outcrossing of hermaphrodites with males (androdioecy). For all these reproductive modes, population genetic theory predicts decreased genetic diversity and increased population differentiation. Here we use mitochondrial control region (mtCR) sequences and nuclear microsatellite loci to determine if the difference in reproductive mode affects the high genetic structure typical of persistent founder effects. Previous authors indicated that T. newberryi is androdioecious because populations are composed of hermaphrodites and males, and T. longicaudatus "short" is hermaphroditic or parthenogenetic because males are absent. In our data, T. newberryi and T. longicaudatus "short" populations were highly structured genetically over short geographic distances for mtCR sequences and microsatellite loci (T. newberryi: ΦST = 0.644, FST = 0.252, respectively; T. l. "short": invariant mtCR sequences, FST = 0.600). Differences between the two Triops species in a number of diversity measures were generally consistent with expectations from population genetic theory regarding reproductive mode; however, three of four comparisons were not statistically significant. We conclude the high genetic differentiation between populations is likely due to founder effects and results suggest both species are composed of selfing hermaphrodites with some level of outcrossing; the presence of males in T. newberryi does not appreciably reduce inbreeding. We cannot exclude the possibility that males in T. newberryi are non-reproductive individuals and the two species have the same mating system.

Bird migratory flyways influence the phylogeography of the invasive brine shrimp Artemia franciscana in its native American range

Since Darwin’s time, waterbirds have been considered an important vector for the dispersal of continental aquatic invertebrates. Bird movements have facilitated the worldwide invasion of the American brine shrimp Artemia franciscana, transporting cysts (diapausing eggs), and favouring rapid range expansions from introduction sites. Here we address the impact of bird migratory flyways on the population genetic structure and phylogeography of A. franciscana in its native range in the Americas. We examined sequence variation for two mitochondrial gene fragments (COI and 16S for a subset of the data) in a large set of population samples representing the entire native range of A. franciscana. Furthermore, we performed Mantel tests and redundancy analyses (RDA) to test the role of flyways, geography and human introductions on the phylogeography and population genetic structure at a continental scale. A. franciscana mitochondrial DNA was very diverse, with two main clades, largely corresponding to Pacific and Atlantic populations, mirroring American bird flyways. There was a high degree of regional endemism, with populations subdivided into at least 12 divergent, geographically restricted and largely allopatric mitochondrial lineages, and high levels of population structure (Φ_ST of 0.92), indicating low ongoing gene flow. We found evidence of human-mediated introductions in nine out of 39 populations analysed. Once these populations were removed, Mantel tests revealed a strong association between genetic variation and geographic distance (i.e., isolation-by-distance pattern). RDA showed that shared bird flyways explained around 20% of the variance in genetic distance between populations and this was highly significant, once geographic distance was controlled for. The variance explained increased to 30% when the factor human introduction was included in the model. Our findings suggest that bird-mediated transport of brine shrimp propagules does not result in substantial ongoing gene flow; instead, it had a significant historical role on the current species phylogeography, facilitating the colonisation of new aquatic environments as they become available along their main migratory flyways.

Molecular phylogeny of the Notostraca

We used a combined analysis of one nuclear (28S rDNA) and three mitochondrial markers (COI, 12S rDNA, 16S rDNA) to infer the molecular phylogeny of the Notostraca, represented by samples from the six continents that are inhabited by this group of branchiopod crustaceans. Our results confirm the monophyly of both extant notostracan genera Triops and Lepidurus with good support in model based and maximum parsimony analyses. We used branchiopod fossils as a calibration to infer divergence times among notostracan lineages and accounted for rate heterogeneity among lineages by applying relaxed-clock models. Our divergence date estimates indicate an initial diversification into the genera Triops and Lepidurus in the Mesozoic, most likely at a minimum age of 152.3-233.5 Ma, i.e., in the Triassic or Jurassic. Implications for the interpretation of fossils and the evolution of notostracan morphology are discussed. We further use the divergence date estimates to formulate a biogeographic hypothesis that explains distributions of extant lineages predominantly by overland dispersal routes. We identified an additional hitherto unrecognised highly diverged lineage within Lepidurus apus lubbocki and three additional previously unknown major lineages within Triops. Within T. granarius we found deep differentiation, with representatives distributed among three major phylogenetic lineages. One of these major lineages comprises T. cancriformis, the T. mauritanicus species group and two hitherto unrecognised T. granarius lineages. Samples that were morphologically identified as T. granarius diverged from the most basal nodes within this major lineage, and divergence dates suggested an approximate age of 23.7-49.6 Ma for T. cancriformis, indicating the need for a taxonomic revision of Triassic and Permian fossils that are currently attributed to the extant T. cancriformis. We thus elevate T. cancriformis minor to full species status as Triops minorTrusheim, 1938 and include in this species the additional Upper Triassic samples that were attributed to T. cancriformis. We further elevate T. cancriformis permiensis to full species status as Triops permiensisGand et al., 1997.

Multiple global radiations in tadpole shrimps challenge the concept of 'living fossils'

'Living fossils', a phrase first coined by Darwin, are defined as species with limited recent diversification and high morphological stasis over long periods of evolutionary time. Morphological stasis, however, can potentially lead to diversification rates being underestimated. Notostraca, or tadpole shrimps, is an ancient, globally distributed order of branchiopod crustaceans regarded as 'living fossils' because their rich fossil record dates back to the early Devonian and their morphology is highly conserved. Recent phylogenetic reconstructions have shown a strong biogeographic signal, suggesting diversification due to continental breakup, and widespread cryptic speciation. However, morphological conservatism makes it difficult to place fossil taxa in a phylogenetic context. Here we reveal for the first time the timing and tempo of tadpole shrimp diversification by inferring a robust multilocus phylogeny of Branchiopoda and applying Bayesian divergence dating techniques using reliable fossil calibrations external to Notostraca. Our results suggest at least two bouts of global radiation in Notostraca, one of them recent, so questioning the validity of the 'living fossils' concept in groups where cryptic speciation is widespread.

High lability of sexual system over 250 million years of evolution in morphologically conservative tadpole shrimps

BACKGROUND

Sexual system is a key factor affecting the genetic diversity, population structure, genome structure and the evolutionary potential of species. The sexual system androdioecy - where males and hermaphrodites coexist in populations - is extremely rare, yet is found in three crustacean groups, barnacles, a genus of clam shrimps Eulimnadia, and in the order Notostraca, the tadpole shrimps. In the ancient crustacean order Notostraca, high morphological conservatism contrasts with a wide diversity of sexual systems, including androdioecy. An understanding of the evolution of sexual systems in this group has been hampered by poor phylogenetic resolution and confounded by the widespread occurrence of cryptic species. Here we use a multigene supermatrix for 30 taxa to produce a comprehensive phylogenetic reconstruction of Notostraca. Based on this phylogenetic reconstruction we use character mapping techniques to investigate the evolution of sexual systems. We also tested the hypothesis that reproductive assurance has driven the evolution of androdioecy in Notostraca.

RESULTS

Character mapping analysis showed that sexual system is an extremely flexible trait within Notostraca, with repeated shifts between gonochorism and androdioecy, the latter having evolved a minimum of five times. In agreement with the reproductive assurance hypothesis androdioecious notostracans are found at significantly higher latitudes than gonochoric ones indicating that post glacial re-colonisation may have selected for the higher colonisation ability conferred by androdioecy.

CONCLUSIONS

In contrast to their conserved morphology, sexual system in Notostraca is highly labile and the rare reproductive mode androdioecy has evolved repeatedly within the order. Furthermore, we conclude that this lability of sexual system has been maintained for at least 250 million years and may have contributed to the long term evolutionary persistence of Notostraca. Our results further our understanding of the evolution of androdioecy and indicate that reproductive assurance is a recurrent theme involved in the evolution of this sexual system.

Toward a global phylogeny of the "living fossil" crustacean order of the Notostraca

Tadpole shrimp (Crustacea, Notostraca) are iconic inhabitants of temporary aquatic habitats worldwide. Often cited as prime examples of evolutionary stasis, surviving representatives closely resemble fossils older than 200 mya, suggestive of an ancient origin. Despite significant interest in the group as 'living fossils' the taxonomy of surviving taxa is still under debate and both the phylogenetic relationships among different lineages and the timing of diversification remain unclear. We constructed a molecular phylogeny of the Notostraca using model based phylogenetic methods. Our analyses supported the monophyly of the two genera Triops and Lepidurus, although for Triops support was weak. Results also revealed high levels of cryptic diversity as well as a peculiar biogeographic link between Australia and North America presumably mediated by historic long distance dispersal. We concluded that, although some present day tadpole shrimp species closely resemble fossil specimens as old as 250 mya, no molecular support was found for an ancient (pre) Mesozoic radiation. Instead, living tadpole shrimp are most likely the result of a relatively recent radiation in the Cenozoic era and close resemblances between recent and fossil taxa are probably the result of the highly conserved general morphology in this group and of homoplasy.

Mitochondrial DNA regionalism and historical demography in the extant populations of Chirocephalus kerkyrensis (Branchiopoda: Anostraca)

BACKGROUND

Mediterranean temporary water bodies are important reservoirs of biodiversity and host a unique assemblage of diapausing aquatic invertebrates. These environments are currently vanishing because of increasing human pressure. Chirocephalus kerkyrensis is a fairy shrimp typical of temporary water bodies in Mediterranean plain forests and has undergone a substantial decline in number of populations in recent years due to habitat loss. We assessed patterns of genetic connectivity and phylogeographic history in the seven extant populations of the species from Albania, Corfu Is. (Greece), Southern and Central Italy.

METHODOLOGY/PRINCIPAL FINDINGS

We analyzed sequence variation at two mitochondrial DNA genes (Cytochrome Oxidase I and 16s rRNA) in all the known populations of C. kerkyrensis. We used multiple phylogenetic, phylogeographic and coalescence-based approaches to assess connectivity and historical demography across the whole distribution range of the species. C. kerkyrensis is genetically subdivided into three main mitochondrial lineages; two of them are geographically localized (Corfu Is. and Central Italy) and one encompasses a wide geographic area (Albania and Southern Italy). Most of the detected genetic variation (≈81%) is apportioned among the aforementioned lineages.

CONCLUSIONS/SIGNIFICANCE

Multiple analyses of mismatch distributions consistently supported both past demographic and spatial expansions with the former predating the latter; demographic expansions were consistently placed during interglacial warm phases of the Pleistocene while spatial expansions were restricted to cold periods. Coalescence methods revealed a scenario of past isolation with low levels of gene flow in line with what is already known for other co-distributed fairy shrimps and suggest drift as the prevailing force in promoting local divergence. We recommend that these evolutionary trajectories should be taken in proper consideration in any effort aimed at protecting Mediterranean temporary water bodies.