Molecular signatures of Pleistocene sea-level changes that affected connectivity among freshwater shrimp in Indo-Australian waters

Deep-sea caridean shrimps collected from the South China Sea with emphasizing their phylogenetic relationships

Despite the high biological and ecological diversity of the South China Sea, limited research has been conducted on the deep-sea species diversity of caridean shrimps. Based on the collections from three scientific expeditions conducted in the South China Sea, 31 caridean species, belonging to nine families, were reported, including the identification of two species not previously documented in this region, namely Janicella spinicauda (A. Milne-Edwards, 1883) and Systellaspis curvispina Crosnier, 1988. In addition to morphological features, the COI and 16S gene sequences of these species were analyzed to assess their evolutionary relationships within each family. Phylogenetic analyses, with highest species coverage to date, indicated that similarity in morphological characteristics does not always lead to closer phylogenetic relationships and some defining characteristics for specific taxa are not always synapomorphies but may be the result of convergent evolution. Our results establish reliable evolutionary relationships within specific taxa and highlight the necessity for further taxonomic revisions within these taxa.

Molecular phylogeny and taxonomic position of Macrobrachiumlanchesteri (De Man, 1911), with descriptions of two new species from Thailand (Decapoda, Caridea, Palaemonidae)

Macrobrachiumlanchesteri (De Man, 1911), a translucent freshwater prawn has a wide distribution range throughout mainland Southeast Asia. A high morphological variation and genetic divergence between different geographical M.lanchesteri populations in Thailand have peculiarly extended the uncertainty of species boundaries and blended confusingly with several Macrobrachium species. To clarify these circumstances, broad sample examinations of the morphological variation, including topotype specimens, and phylogenetic reconstruction based on the concatenated mitochondrial dataset (16s rRNA and COI genes) were performed. Broad morphological examination of M.lanchesteri has shown congruency with phylogenetic analyses by revealing prominent lineages of M.lanchesteri sensu stricto and two new sibling lineages with interspecific variation between 6.48-8.76% for COI and 3.06-4.23% for 16S. Descriptions of two new species, named herein as M.panhai Chaowvieng & Siriwut, sp. nov. and M.rostrolevatus Chaowvieng & Siriwut, sp. nov. are provided. Morphological investigation of rostral form suggested plasticity in M.rostrolevatus populations showing the morphological trait associated with their habitat preferences. Furthermore, phylogenetic positions of the three taxa affirmed the hidden diversity of Thai freshwater Macrobrachium fauna correlated with the river network in the Mekong and Chao Phraya basins, Thailand. The genetic data and distribution records obtained in this study may also assist future river conservation plans as well as the sustainable management of freshwater prawn diversity.

Genomic analysis reveals strong population structure in the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865))

Australia is home to over 140 species of freshwater crayfish (Decapoda: Parastacidae), representing a centre of diversity for this group in the Southern Hemisphere. Species delimitation in freshwater crayfish is difficult because many species show significant variation in colouration and morphology. This is particularly evident in the genus Euastacus, which exhibits large variations in colour and spination throughout its putative range. To understand this variation, we investigated the genetic diversity, population structure, phylogeny, and evolutionary timescale of the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865)). Our data set is sampled from over 70 individuals from across the ∼600 km range of the species, and includes a combination of two mitochondrial markers and more than 7000 single-nucleotide polymorphisms (SNPs) from the nuclear genome. Data were also obtained for representatives of the close relative, Euastacus vesper McCormack and Ahyong, 2017. Genomic SNP analyses revealed strong population structure, with multiple distinct populations showing little evidence of gene flow or migration. Phylogenetic analyses of mitochondrial data revealed similar structure between populations. Taken together, our analyses suggest that E. spinifer, as currently understood, represents a species complex, of which E. vesper is a member. Molecular clock estimates place the divergences within this group during the Pleistocene. The isolated and highly fragmented populations identified in our analyses probably represent relict populations of a previously widespread ancestral species. Periodic flooding events during the Pleistocene are likely to have facilitated the movement of these otherwise restricted freshwater crayfish within and between drainage basins, including the Murray-Darling and South East Coast Drainages. We present evidence supporting the recognition of populations in the southern parts of the range of E. spinifer as one or two separate species, which would raise the number of species within the E. spinifer complex to at least three. Our results add to the growing body of evidence that many freshwater crayfish exhibit highly fragmented, range-restricted distributions. In combination with the life-history traits of these species, the restricted distributions exacerbate the threats already placed on freshwater crayfish, which are among the five most endangered animal groups globally.

Two new hermit crab species of Diogenes (Crustacea: Decapoda: Diogenidae) from Atlanto‐Mediterranean coasts of Iberian Peninsula: Poleward migrants or merely overlooked indigenous species?

A new hermit crab species of the genus Diogenes with reddish‐orange cheliped, Diogenes erythromanus sp. nov., is described and illustrated based on specimens from the Mediterranean coasts of the Iberian Peninsula, southern Spain. In addition, a second morphotype originating from Mauritanian waters and morphologically very close to D. erythromanus sp. nov. is described as a different species, D. arguinensis sp. nov. The new species are here compared to morphologically similar congeners, especially to those inhabiting the same geographical range. Diogenes erythromanus sp. nov. is distinguishable from other Diogenes primarily by the shape and armature of the left cheliped, with a palm slightly higher than long, with a ridge of spines running along the proximal lower margin that continues with a series of spinose rows forming a central band parallel to the upper margin of the palm. The palm in D. arguinensis sp. nov. is longer than high and shows similar proximal ridge, but without central spinose ridge. The shape of the cheliped is also different in D. arguinensis sp. nov., with long dactylus, which is also flattened and twisted. Sequences from two mitochondrial and one nuclear genes, and comparative analyses with other available sequences for the genus, are also included. Molecular phylogenetic analyses support the morphological delimitation, with D. erythromanus sp. nov. and D. arguinensis sp. nov. forming a separate group, more related to other tropical species, which raises different possible explanations for its presence in the Iberian Peninsula.

Molecular ecology of the fiddler crab Austruca perplexa (H. Milne Edwards, 1852): genetic divergence along a major biogeographical barrier, Wallace’s Line

Genetic diversity and population structure in the fiddler crab Austruca perplexa were investigated to acquire a better understanding of the evolutionary history of the species. Nucleotide sequence analysis was performed from a polymerase chain reaction-amplified fragment of the mitochondrial DNA control region. A 691 bp nucleotide sequence was obtained from 618 specimens collected from 13 sites across Japan, Taiwan, the Philippines, Indonesia and Australia. Haplotype diversity ranged from 0.8 to 0.99, and nucleotide diversity values were lower (range, 0.30–1.9%) than those reported previously for other crustacean taxa. Gene flow was evident within populations in Japan and western Indonesia, but absent among all other populations, including eastern Indonesia. This pattern conforms to the one observed in many other marine taxa across the major biogeographical region referred to as Wallacea. The population pairwise fixation index (FST) and FST  P-values were high and significant among many sites, implying that gene flow is restricted among most of the geographical regions sampled here. We hypothesize that physical oceanic barriers coupled with a short pelagic larval duration are responsible for creating the patterns we found. Strong evidence for population structure in a species that has relatively high dispersal potential, resulting in among-population differentiation, is a potential driver of evolutionary novelty. Our results provide a foundation for developing better conservation strategies for this widespread intertidal species.

Evidence of cryptic diversity in freshwater Macrobrachium prawns from Indochinese riverine systems revealed by DNA barcode, species delimitation and phylogenetic approaches

The diversity of Indochinese prawns in genus Macrobrachium is enormous due to the habitat diversification and broad tributary networks of two river basins: the Chao Phraya and the Mekong. Despite long-standing interest in SE-Asian decapod diversity, the subregional Macrobrachium fauna is still not yet comprehensively clarified in terms of taxonomic identification or genetic diversification. In this study, integrative taxonomic approaches including morphological examination, DNA barcoding, and molecular species delimitation were used to emphasize the broad scale systematics of Macrobrachium prawns in Indochina. Twenty-seven nominal species were successfully re-verified by traditional and molecular taxonomy. Barcode gap analysis supported broad overlapping of species boundaries. Taxonomic ambiguity of several deposited samples in the public database is related to inter- and intraspecific genetic divergence as indicated by BOLD discordance. Diagnostic nucleotide positions were found in six Macrobrachium species. Eighteen additional putative lineages are herein assigned using the consensus of species delimitation methods. Genetic divergence indicates the possible existence of cryptic species in four morphologically complex and wide-ranging species: M. lanchesteri, M. niphanae, M. sintangense, and some members of the M. pilimanus group. The geographical distribution of some species supports the connections and barriers attributed to paleo-historical events of SE-Asian rivers and land masses. Results of this study show explicitly the importance of freshwater ecosystems in Indochinese subregions, especially for the Mekong River Basin due to its high genetic diversity and species composition found throughout its tributaries.

Molecular phylogeny and species delimitation of the freshwater prawn Macrobrachium pilimanus species group, with descriptions of three new species from Thailand

Specific status and species boundaries of several freshwater prawns in the Macrobrachium pilimanus species group remain ambiguous, despite the taxonomic re-description of type materials and additional specimens collected to expand the boundaries of some species. In this study, the "pilimanus" species group of Macrobrachium sensu Johnson (1958) was studied using specimens collected from montane streams of Thailand. Molecular phylogenetic analyses based on sequences of three molecular markers (COI, 16S and 18S rRNA) were performed. The phylogenetic results agreed with morphological identifications, and indicated the presence of at least nine putative taxa. Of these, six morphospecies were recognised as M. malayanum, M. forcipatum, M. dienbienphuense, M. hirsutimanus, M. eriocheirum, and M. sirindhorn. Furthermore, three morphologically and genetically distinct linages were detected, and are described herein as M. naiyanetri Siriwut sp. nov. , M. palmopilosum Siriwut sp. nov. and M. puberimanus Siriwut sp. nov. The taxonomic comparison indicated wide morphological variation in several species and suggested additional diagnostic characters that are suitable for use in species diagnoses, such as the shape and orientation of fingers, the rostrum form, and the presence or absence of velvet pubescence hairs and tuberculated spinulation on each telopodite of the second pereiopods. The "pilimanus" species group was portrayed as non-monophyletic in both ML and BI analyses. The genetic structure of different geographical populations in Thailand was detected in some widespread species. The species delimitation based on the four delimitation methods (BIN, ABGD, PTP and GMYC) suggested high genetic diversity of the "pilimanus" species group and placed the candidate members much higher than in previous designations based on traditional morphology. This finding suggests that further investigation of morphological and genetic diversity of Southeast Asian freshwater prawns in the genus Macrobrachium is still required to provide a comprehensive species list to guide efforts in conservation and resource management.

Mitochondrial heteroplasmy and pseudogenes in the freshwater prawn, Macrobrachium amazonicum (Heller, 1862): DNA barcoding and phylogeographic implications

The mitochondrial cytochrome oxidase c subunit 1 (COI) gene has been widely used in phylogenetic studies of crustaceans and analyses in population genetics. As COI studies have become more popular, there has been an increase in the number of reports of the presence of nuclear insertions of mitochondrial DNA (Numts) and mitochondrial heteroplasmy. Here, we provide evidence of both types of event in the COI sequences of Macrobrachium amazonicum, an economically important freshwater prawn, which is widespread in South America. Heteroplasmy and Numts were confirmed by different methods of DNA extraction (genomic, mitochondrial, and nuclear-enriched DNA), cloning, and sequencing, and were observed in 11 of the 14 populations sampled, primarily in the Amazon region. We discuss how the occurrence of these events affects the interpretation of the genetic relationships among the M. amazonicum populations, and we recommend caution when using COI for genetic inferences in prawns of the genus Macrobrachium, and in particular that any analysis should include nuclear markers.

Miocene geologic dynamics of the Australian Sahul Shelf determined the biogeographic patterns of freshwater planorbid snails (Miratestinae) in the Indo-Australian Archipelago

The complex geological and climatic processes that have shaped the Indo-Australian Archipelago since the Cenozoic likely also gave rise to its species-rich biota. Strictly freshwater organisms might be particularly suitable for understanding the influence of these abiotic factors on their biogeography in such a insular setting as their distribution may reflect past abiotic events at large and small geographical scales. We here investigate the historical biogeography of the Miratestinae, a subfamily of Planorbidae. These freshwater gastropods are widely distributed in the eastern IAA from Australia, New Guinea, the Moluccas, and Sulawesi to the Philippines. The first comprehensive molecular phylogeny of the Miratestinae was inferred based on two mitochondrial and two nuclear genetic markers using maximum likelihood and Bayesian inference. Four species delimitation methods were applied to identify molecular operational taxonomic units (MOTUs). Divergence times were inferred using an uncorrelated lognormal relaxed-clock model by applying a taxon- and marker-specific substitution rate. Ancestral geographic ranges were estimated based on the dated phylogeny using BioGeoBEARS. The species delimitation revealed a total of 23 MOTUs, 16 of which might represent species new to science. The BioGeoBEARS analyses suggest an Australian origin for the Miratestinae at c. 22 Ma and identified jump dispersal to be the main process of colonization. The first colonization events from Australia to the IAA occurred in the Middle-Late Miocene (12-13 Ma), whereas intra-island diversification took mainly place since the Late Miocene-Pliocene. Colonization and diversification events remarkably coincide with major geologic events that shaped the geography of the region. The increasing availability of landmasses along the Sahul Shelf likely promoted stepping-stone dispersal to New Guinea, Sulawesi and the Philippines as early as the islands emerged. Major geological and climatic events such as the amalgamation of the island Sulawesi, the regional aridification in Australia or the uplift of massive mountain ranges in New Guinea likely played a considerable role for intra-island diversification.

Genetic and Morphological Characterization of Freshwater Shrimps (Caridina africana Kingsley, 1882) Reveals the Presence of Alien Shrimps in the Cape Floristic Region, South Africa

Morphological identification and molecular data (mtDNA COI) were used to resolve the taxonomic identity of a non-native freshwater shrimp in the Cape Floristic Region (CFR) of South Africa and to evaluate levels of genetic diversity and differentiation in the species' core natural distribution. The species was morphologically and genetically identified as Caridina africana Kingsley, 1882, whose main natural distribution is in the KwaZulu-Natal (KZN) Province, more than 1200 km from the point of new discovery. Subsequently, sequence data from natural populations occurring in seven rivers throughout KZN showed the presence of nuclear copies of the mtDNA COI gene (NUMTs) in 46 out of 140 individuals. Upon removal of sequences containing NUMTs, levels of genetic diversity were low in the alien population (possibly as a consequence of a bottleneck event), while varying levels of genetic diversity and differentiation were found in natural populations, indicating habitat heterogeneity, fragmentation and restricted gene flow between rivers. Following the present study, the alien shrimp has survived the Western Cape's winter and dispersed into a nearby tributary of the Eerste River System, hence posing an additional potential threat to endangered endemics. Understanding the biology of this alien species will aid detection and eradication procedures.

Phylogeography of Cuban Rivulus: evidence for allopatric speciation and secondary dispersal across a marine barrier

The genus Rivulus is currently comprised of two species, R. cylindraceus and R. insulaepinorum, which are endemic to Cuba. However, the taxonomic status of the latter species remains dubious because of the poor quality of the original description. In addition, a recent barcoding survey suggests that the two species may be conspecific. The aim of this study was to test the hypothesis that the two species represent a single evolutionary clade. To delimit the species and their evolutionary history, we used a combination of molecular phylogenetic analyses, with both mitochondrial and nuclear sequences, tests of phylogeographic hypotheses, combined with morphological measurements and information on known dispersal barriers and species distribution. None of the data sets support R. insulaepinorum and R. cylindraceus as separate taxa. However, a new species, restricted to the northwestern part of the main island, was identified by phylogenetic analyses, body colour pattern and geographical distribution. The evolutionary distance between the two lineages (cytb, d=15%; CAM-4, d=2.5%) indicates a long period of divergence. Phylogeographic analyses shed light on the dispersal history of R. cylindraceus, which probably originated on the Isla de la Juventud. They also suggest that each lineage had contrasting histories; Rivulus sp. is restricted to a relatively small geographic area whereas R. cylindraceus has dispersed considerably and more than once from its centre of origin, probably facilitated by sea level fluctuations. These results strengthen previous findings, i.e. that the diversity of Cuban freshwater fishes is far from well-known and deserves more in-depth studies, and that vicariance and dispersal events have resulted in a complex biogeographical landscape which has had a significant impact on the freshwater fishes of the Caribbean islands.

Contrasting genetic structure among populations of two amphidromous fish species (Sicydiinae) in the Central West Pacific

Both present-day and past processes can shape connectivity of populations. Pleistocene vicariant events and dispersal have shaped the present distribution and connectivity patterns of aquatic species in the Indo-Pacific region. In particular, the processes that have shaped distribution of amphidromous goby species still remain unknown. Previous studies show that phylogeographic breaks are observed between populations in the Indian and Pacific Oceans where the shallow Sunda shelf constituted a geographical barrier to dispersal, or that the large spans of open ocean that isolate the Hawaiian or Polynesian Islands are also barriers for amphidromous species even though they have great dispersal capacity. Here we assess past and present genetic structure of populations of two amphidromous fish (gobies of the Sicydiinae) that are widely distributed in the Central West Pacific and which have similar pelagic larval durations. We analysed sections of mitochondrial COI, Cytb and nuclear Rhodospine genes in individuals sampled from different locations across their entire known range. Similar to other Sicydiinae fish, intraspecific mtDNA genetic diversity was high for all species (haplotype diversity between 0.9–0.96). Spatial analyses of genetic variation in Sicyopus zosterophorum demonstrated strong isolation across the Torres Strait, which was a geologically intermittent land barrier linking Australia to Papua New Guinea. There was a clear genetic break between the northwestern and the southwestern clusters in Si. zosterophorum (φ_ST = 0.67502 for COI) and coalescent analyses revealed that the two populations split at 306 Kyr BP (95% HPD 79–625 Kyr BP), which is consistent with a Pleistocene separation caused by the Torres Strait barrier. However, this geographical barrier did not seem to affect Sm. fehlmanni. Historical and demographic hypotheses are raised to explain the different patterns of population structure and distribution between these species. Strategies aiming to conserve amphidromous fish should consider the presence of cryptic evolutionary lineages to prevent stock depletion.

Multiple colonizations lead to cryptic biodiversity in an island ecosystem: comparative phylogeography of anchialine shrimp species in the Ryukyu Archipelago, Japan

Archipelagos of the Indo-West Pacific are considered to be among the richest in the world in biodiversity, and phylogeographic studies generally support either the center of origin or the center of accumulation hypothesis to explain this pattern. To differentiate between these competing hypotheses for organisms from the Indo-West Pacific anchialine ecosystem, defined as coastal bodies of mixohaline water fluctuating with the tides but having no direct oceanic connections, we investigated the genetic variation, population structure, and evolutionary history of three caridean shrimp species (Antecaridina lauensis, Halocaridinides trigonophthalma, and Metabetaeus minutus) in the Ryukyu Archipelago, Japan. We used two mitochondrial genes--cytochrome c oxidase subunit I (COI) and large ribosomal subunit (16S-rDNA)--complemented with genetic examination of available specimens from the same or closely related species from the Indian and Pacific Oceans. In the Ryukyus, each species encompassed 2-3 divergent (9.52%-19.2% COI p-distance) lineages, each having significant population structure and varying geographic distributions. Phylogenetically, the A. lauensis and M. minutus lineages in the Ryukyus were more closely related to ones from outside the archipelago than to one another. These results, when interpreted in the context of Pacific oceanographic currents and geologic history of the Ryukyus, imply multiple colonizations of the archipelago by the three species, consistent with the center of accumulation hypothesis. While this study contributes toward understanding the biodiversity, ecology, and evolution of organisms in the Ryukyus and the Indo-West Pacific, it also has potential utility in establishing conservation strategies for anchialine fauna of the Pacific Basin in general.

Evolutionary drivers of diversification and distribution of a southern temperate stream fish assemblage: testing the role of historical isolation and spatial range expansion

This study used phylogenetic analyses of mitochondrial cytochrome b sequences to investigate genetic diversity within three broadly co-distributed freshwater fish genera (Galaxias, Pseudobarbus and Sandelia) to shed some light on the processes that promoted lineage diversification and shaped geographical distribution patterns. A total of 205 sequences of Galaxias, 177 sequences of Pseudobarbus and 98 sequences of Sandelia from 146 localities across nine river systems in the south-western Cape Floristic Region (South Africa) were used. The data were analysed using phylogenetic and haplotype network methods and divergence times for the clades retrieved were estimated using *BEAST. Nine extremely divergent (3.5-25.3%) lineages were found within Galaxias. Similarly, deep phylogeographic divergence was evident within Pseudobarbus, with four markedly distinct (3.8-10.0%) phylogroups identified. Sandelia had two deeply divergent (5.5-5.9%) lineages, but seven minor lineages with strong geographical congruence were also identified. The Miocene-Pliocene major sea-level transgression and the resultant isolation of populations in upland refugia appear to have driven widespread allopatric divergence within the three genera. Subsequent coalescence of rivers during the Pleistocene major sea-level regression as well as intermittent drainage connections during wet periods are proposed to have facilitated range expansion of lineages that currently occur across isolated river systems. The high degree of genetic differentiation recovered from the present and previous studies suggest that freshwater fish diversity within the south-western CFR may be vastly underestimated, and taxonomic revisions are required.

Australasian sky islands act as a diversity pump facilitating peripheral speciation and complex reversal from narrow endemic to widespread ecological supertramp

The Australasian archipelago is biologically extremely diverse as a result of a highly puzzling geological and biological evolution. Unveiling the underlying mechanisms has never been more attainable as molecular phylogenetic and geological methods improve, and has become a research priority considering increasing human-mediated loss of biodiversity. However, studies of finer scaled evolutionary patterns remain rare particularly for megadiverse Melanesian biota. While oceanic islands have received some attention in the region, likewise insular mountain blocks that serve as species pumps remain understudied, even though Australasia, for example, features some of the most spectacular tropical alpine habitats in the World. Here, we sequenced almost 2 kb of mitochondrial DNA from the widespread diving beetle Rhantus suturalis from across Australasia and the Indomalayan Archipelago, including remote New Guinean highlands. Based on expert taxonomy with a multigene phylogenetic backbone study, and combining molecular phylogenetics, phylogeography, divergence time estimation, and historical demography, we recover comparably low geographic signal, but complex phylogenetic relationships and population structure within R. suturalis. Four narrowly endemic New Guinea highland species are subordinated and two populations (New Guinea, New Zealand) seem to constitute cases of ongoing speciation. We reveal repeated colonization of remote mountain chains where haplotypes out of a core clade of very widespread haplotypes syntopically might occur with well-isolated ones. These results are corroborated by a Pleistocene origin approximately 2.4 Ma ago, followed by a sudden demographic expansion 600,000 years ago that may have been initiated through climatic adaptations. This study is a snapshot of the early stages of lineage diversification by peripatric speciation in Australasia, and supports New Guinea sky islands as cradles of evolution, in line with geological evidence suggesting very recent origin of high altitudes in the region.

Transcriptomics of a giant freshwater prawn (Macrobrachium rosenbergii): de novo assembly, annotation and marker discovery

BACKGROUND

Giant freshwater prawn (Macrobrachium rosenbergii or GFP), is the most economically important freshwater crustacean species. However, as little is known about its genome, 454 pyrosequencing of cDNA was undertaken to characterise its transcriptome and identify genes important for growth.

METHODOLOGY AND PRINCIPAL FINDINGS

A collection of 787,731 sequence reads (244.37 Mb) obtained from 454 pyrosequencing analysis of cDNA prepared from muscle, ovary and testis tissues taken from 18 adult prawns was assembled into 123,534 expressed sequence tags (ESTs). Of these, 46% of the 8,411 contigs and 19% of 115,123 singletons possessed high similarity to sequences in the GenBank non-redundant database, with most significant (E value < 1e(-5)) contig (80%) and singleton (84%) matches occurring with crustacean and insect sequences. KEGG analysis of the contig open reading frames identified putative members of several biological pathways potentially important for growth. The top InterProScan domains detected included RNA recognition motifs, serine/threonine-protein kinase-like domains, actin-like families, and zinc finger domains. Transcripts derived from genes such as actin, myosin heavy and light chain, tropomyosin and troponin with fundamental roles in muscle development and construction were abundant. Amongst the contigs, 834 single nucleotide polymorphisms, 1198 indels and 658 simple sequence repeats motifs were also identified.

CONCLUSIONS

The M. rosenbergii transcriptome data reported here should provide an invaluable resource for improving our understanding of this species' genome structure and biology. The data will also instruct future functional studies to manipulate or select for genes influencing growth that should find practical applications in aquaculture breeding programs.

Evolution of life history traits in Asian freshwater prawns of the genus Macrobrachium (Crustacea: Decapoda: Palaemonidae) based on multilocus molecular phylogenetic analysis

Freshwater prawns of the genus Macrobrachium are free-living decapod crustaceans that are commonly encountered in tropical streams and lakes. We present a molecular phylogenetic analysis of the diverse Southeast and East Asian fauna based on >3 kb sequence data from three nuclear and two mitochondrial markers for almost 50% of the described fauna. We reconstruct the phylogenetic relationships and track the evolution of key life history traits. Our tree suggests that the last common ancestor of the Asian Macrobrachium laid numerous small eggs and had prolonged larval development ("PLD") in saline coastal waters after which the adults matured in freshwater habitats. We also argue for five independent losses of the marine larval phase to yield five clades of species that develop entirely in freshwater and have fewer and larger eggs than the species with PLD. These species have either semi-abbreviated (two origins) with at least one free-swimming stage or abbreviated larval development ("ALD": three origins) which lack free-swimming larvae. A Shimodaira-Hasegawa test rejects all trees that would imply a single loss of the marine larval phase, but alternative and equally parsimonious optimizations exist that imply a smaller number of losses. However, these scenarios would require the re-acquisition of free-swimming larvae. A concentrated-change test supports Pereira and Garcia's [Pereira, G.A., Garcia, J.V., 1995. Larval development of Macrobrachium reyesi Pereira (Decapoda, Palaemonidae), with a discussion on the origin of abbreviated development in palaemonids. J. Crust. Biol. 15, 117-133] hypothesis of a significant correlation between living in freshwater and the origin of semi-abbreviated and abbreviated larval development. Our phylogenetic tree also reveals that Asian Macrobrachium have independently become cavernicolous at least twice, and invaded the highly acidic waters of freshwater and peat swamps two or three times.