Two centuries of biodiversity discovery and loss in Singapore.

There is an urgent need for reliable data on the impacts of deforestation on tropical biodiversity. The city-state of Singapore has one of the most detailed biodiversity records in the tropics, dating back to the turn of the 19th century. In 1819, Singapore was almost entirely covered in primary forest, but this has since been largely cleared. We compiled more than 200 y of records for 10 major taxonomic groups in Singapore (>50,000 individual records; >3,000 species), and we estimated extinction rates using recently developed and novel statistical models that account for "dark extinctions," i.e., extinctions of undiscovered species. The estimated overall extinction rate was 37% (95% CI [31 to 42%]). Extrapolating our Singapore observations to a future business-as-usual deforestation scenario for Southeast Asia suggests that 18% (95% CI [16 to 22%]) of species will be lost regionally by 2100. Our extinction estimates for Singapore and Southeast Asia are a factor of two lower than previous estimates that also attempted to account for dark extinctions. However, we caution that particular groups such as large mammals, forest-dependent birds, orchids, and butterflies are disproportionately vulnerable.

Diversification of freshwater crabs on the sky islands in the Hengduan Mountains Region, China.

The numerous naturally-fragmented sky islands (SIs) in the Hengduan Mountains Region (HMR) of southwestern China constitute discontinuous landscapes where montane habitats are isolated by dry-hot valleys which have fostered exceptional species diversification and endemicity. However, studies documenting the crucial role of SI on the speciation dynamics of native freshwater organisms are scarce. Here we used a novel set of comprehensive genetic markers (24 nuclear DNA sequences and complete mitogenomes), morphological characters, and biogeographical information to reveal the evolutionary history and speciation mechanisms of a group of small-bodied montane potamids in the genus Tenuipotamon. Our results provide a robustly supported phylogeny, and suggest that the vicariance events of these montane crabs correlate well with the emergence of SIs due to the uplift of the HMR during the Late Oligocene. Furthermore, ancestrally, mountain ridges provided corridors for the dispersal of these montane crabs that led to the colonization of moist montane-specific habitats, aided by past climatic conditions that were the crucial determinants of their evolutionary history. The present results illustrated that the mechanisms isolating SIs are reinforced by the harsh-dry isolating climatic features of dry-hot valleys separating SIs and continue to affect local diversification. This offers insights into the causes of the high biodiversity and endemism shown by the freshwater crabs of the HMR-SIs in southwestern China.

Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments.

For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood, and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7,600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least seven and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways.

Allopatric mosaics in the Indo-West Pacific crab subfamily Chlorodiellinae reveal correlated patterns of sympatry, genetic divergence, and genitalic disparity.

Molecular studies have revealed that many species once thought to be wide-ranging in the Indo-West Pacific contain allopatric mosaics of endemic lineages. These lineages provide compelling evidence that substantial time is needed to evolve isolating mechanisms sufficient to permit successful secondary sympatry, and that divergence is initiated in allopatry. In this context, questions arise regarding the nature, timing, and origin of isolating mechanisms that permit secondary sympatry. We present a phylogeny of the crab subfamily Chlorodiellinae which displays allopatric mosaics within species. These allopatric lineages typically do not have divergent male genitalia, while older sympatric lineages do. We tested the relationship between genetic distance (proxy for time), sympatry, and the divergence of male genitalic morphology. Our results suggest that male genitalic divergence is not involved in the initiation of speciation in chlorodielline crabs, having likely occurred only after isolation began in allopatry. However, morphological evolution of genitalia seemingly does play an important role in completing the process of speciation in these crabs.

Shift in symbiotic lifestyle as the major process shaping the evolution of pea crabs (Decapoda: Brachyura: Pinnotheroidea).

The pea crabs, superfamily Pinnotheroidea, are exceptional among brachyuran crabs in their diverse symbiotic associations involving both inquilinism and protective symbiosis. While this group presents a rare opportunity for evolutionary comparative study of host switching and morphological evolution in marine macroinvertebrates, previous phylogenetic studies have been focused on systematics. Here, we reconstructed the most extensive phylogeny of Pinnotheroidea based on two mitochondrial and six nuclear markers, with the aim of elucidating the host switching pathways and the correlation between symbiotic lifestyles and selected morphological adaptations. Ancestral state reconstruction of host association revealed a monophyletic origin of symbiosis in the form of inquilinism. Subsequent shifts in microhabitat preference for burrows or worm tubes, and the move to protective symbiosis, primarily in the switch to mollusc endosymbiosis, contributed to radiation in Pinnotheridae. Further parallel colonisations of echinoderms and tunicates occurred but did not lead to extensive diversification, except in the Clypeasterophilus + Dissodactylus lineage, which experienced a unique switch to echinoderm ectosymbiosis. The evolution of the third maxillipeds, carapace shape and ambulatory pereiopods suggests a rather strong coupling with the symbiotic lifestyle (whether inquilinism or protective symbiosis). Phenotypic diversity of these characters was higher among species engaged in protective symbiosis, with convergence in form (or function) among those sharing the same host affiliation. Species having different host affiliations or symbiotic lifestyles might also exhibit convergence in the form of the three morphological traits, suggesting a common adaptive value of the specialisations. Pinnotherid crabs overall exhibited a lower trait diversity than the also symbiotic palaemonid shrimps with comparable species diversity. This may plausibly be attributed to differences in potential for morphological modification to serve additional functions among the traits analysed in the two groups, the less frequent host switching and the less diverse host affiliations, and thus a less complicated evolutionary history in pinnotherids.

Molecular phylogeny of Thoracotremata crabs (Decapoda, Brachyura): Toward adopting monophyletic superfamilies, invasion history into terrestrial habitats and multiple origins of symbiosis.

The Thoracotremata is a large and successful group of "true" crabs (Decapoda, Brachyura, Eubrachyura) with a great diversity of lifestyles and well-known intertidal representatives. The group represents the largest brachyuran radiation into terrestrial and semi-terrestrial environments and comprises multiple lineages of obligate symbiotic species. In consequence, they exhibit very diverse physiological and morphological adaptations. Our understanding of their evolution is, however, largely obscured by their confused classification. Here, we resolve interfamilial relationships of Thoracotremata, using 10 molecular markers and exemplars from all nominal families in order to reconstruct the pathways of lifestyle transition and to prepare a new taxonomy corresponding to phylogenetic relationships. The results confirm the polyphyly of three superfamilies as currently defined (Grapsoidea, Ocypodoidea and Pinnotheroidea). At the family level, Dotillidae, Macrophthalmidae, and Varunidae are not monophyletic. Ancestral state reconstruction analyses and divergent time estimations indicate that the common ancestor of thoracotremes already thrived in intertidal environments in the Late Cretaceous and terrestrialization became a major driver of thoracotreme diversification. Multiple semi-terrestrial and terrestrial lineages originated and radiated in the Early Eocene, coinciding with the global warming event at the Paleocene-Eocene Thermal Maximum (PETM). Secondary invasions into subtidal regions and colonizations of freshwater habitats occurred independently through multiple semi-terrestrial and terrestrial lineages. Obligate symbiosis between thoracotremes and other marine macro-invertebrates evolved at least twice. On the basis of the current molecular phylogenetic hypothesis, it will be necessary in the future to revise and recognize seven monophyletic superfamilies and revisit the morphological character states which define them.

A comprehensive molecular phylogeny of the brachyuran crab superfamily Xanthoidea provides novel insights into its systematics and evolutionary history.

Maximum likelihood and Bayesian phylogenies for the brachyuran crab superfamily Xanthoidea were estimated based on three mitochondrial and four nuclear genes to infer phylogenetic relationships and inform taxonomy. Habitat data was then used in conjunction with several diversification rates analyses (BAMM, BiSSE, HiSSE, and FiSSE) to test evolutionary hypotheses regarding the diversification of xanthoid crabs. The phylogenies presented are the most comprehensive to date in terms of global diversity as they include all four constituent families (Xanthidae, Panopeidae, Pseudorhombilidae, and Linnaeoxanthidae) spanning all oceans in which xanthoid crabs occur. Six Xanthoidea families are recognised. Panopeidae and Xanthidae sensu stricto are the two largest family-level clades, which are reciprocally monophyletic. Pseudorhombilidae is nested within and is here treated as a subfamily of Panopeidae. Former subfamilies or tribes of Xanthidae sensu lato are basally positioned clades in Xanthoidea and are here assigned family-level ranks: Garthiellidae, Linnaeoxanthidae, Antrocarcinidae, and Nanocassiopidae. The genera Linnaeoxantho and Melybia were recovered in separate clades with Linnaeoxantho being sister to the family Antrocarcinidae, while Melybia was recovered within the family Panopeidae. The existing subfamily classification of Xanthidae and Panopeidae is drastically restructured with 20 xanthid and four panopeid subfamilies provisionally recognised. Diversification-time analyses inferred the origin of Xanthoidea and Garthiellidae in the Eocene, while the other families originated during the Oligocene. The majority of genus- and species-level diversification took place during the Miocene. Ancestral state reconstruction based on depth of occurrence (shallow vs. deep water) shows some ambiguity for the most recent common ancestor of Xanthoidea and Nanocassiopidae. The most recent common ancestors of Antrocarcinidae and Panopeidae were likely deep-water species, while those of Garthiellidae and Xanthidae were probably shallow-water species. Several shifts in net diversification rates were detected but they were not associated with depth-related habitat transitions.

Phylogenomic analyses of brachyuran crabs support early divergence of primary freshwater crabs.

Recent fossil calibrated molecular phylogenies have revealed that the Brachyura underwent rapid radiation during the Cretaceous and Early Tertiary, resulting in many early diverging lineages separated by short internodes that remain difficult to resolve. Here we present the first phylogenomic analyses of Brachyura using transcriptome data from 30 brachyuran species and 22 families. Analyses were carried out on a dataset containing 372 putative homologous loci (246,590 bps) and included data from 21 newly generated transcriptomes. With minor exceptions, all phylogenetic analyses recovered a congruent, highly resolved and well supported brachyuran phylogeny. Consistent with previous work, this phylogeny suggests that primary freshwater crabs diverged early in brachyuran evolution, falling sister to Thoracotremata, thus supporting recent proposal for establishment of subsection Potamoida for primary freshwater crabs. The interfamilial relationships among heterotremes were well resolved in our analyses but those within Thoracotremata remained problematic. Phylogenomic analyses clearly provide a powerful means for resolving brachyuran relationships, but future studies would benefit greatly from increased taxon sampling of transcriptome data.

Evolutionary history of true crabs (Crustacea: Decapoda: Brachyura) and the origin of freshwater crabs.

Crabs of the infra-order Brachyura are one of the most diverse groups of crustaceans with approximately 7,000 described species in 98 families, occurring in marine, freshwater, and terrestrial habitats. The relationships among the brachyuran families are poorly understood due to the high morphological complexity of the group. Here, we reconstruct the most comprehensive phylogeny of Brachyura to date using sequence data of six nuclear protein-coding genes and two mitochondrial rRNA genes from more than 140 species belonging to 58 families. The gene tree confirms that the "Podotremata," are paraphyletic. Within the monophyletic Eubrachyura, the reciprocal monophyly of the two subsections, Heterotremata and Thoracotremata, is supported. Monophyly of many superfamilies, however, is not recovered, indicating the prevalence of morphological convergence and the need for further taxonomic studies. Freshwater crabs were derived early in the evolution of Eubrachyura and are shown to have at least two independent origins. Bayesian relaxed molecular methods estimate that freshwater crabs separated from their closest marine sister taxa ~135 Ma, that is, after the break up of Pangaea (∼200 Ma) and that a Gondwanan origin of these freshwater representatives is untenable. Most extant families and superfamilies arose during the late Cretaceous and early Tertiary.

The land crabs of the Discoplax longipes A. Milne-Edwards, 1867 species group, with description of a new species from Guam (Crustacea: Decapoda: Brachyura: Gecarcinidae).

Specimens of the gecarcinid land crab Discoplax longipes A. Milne-Edwards, 1867, from the western Pacific, can be separated into two distinct groups on the basis of DNA (mitochondrial 16S rDNA and cytochrome oxidase subunit I) and structure of the male first gonopod. On the basis of this data, the material that occurs from the Loyalty Islands to French Polynesia is shown to be D. longipes s. str., whereas specimens from Guam are here referred to a new pseudocryptic species, D. michalis n. sp. The two species are described and figured; and a revised key to the long-legged Discoplax species is provided.

Notes on Hexapodidae (Crustacea, Brachyura) from Indonesia and Malaysia, with description of a new species of Mariaplax Rahayu & Ng, 2014, from Lombok, Indonesia.

The male of Hexapinus latipes (De Haan, 1835), so far known only from female specimens, is described based on the material reported by De Man (1888) as "Hexapus sexpes". Material referred to "Hexapus sexpes" by Tesch (1918) is shown instead to belong to Hexapinus simplex Rahayu & Ng, 2014, and Hexapinus latus Rahayu & Ng, 2014, while his "Hexaplax megalops Doflein, 1904" belongs to Hexaplax aurantium Rahayu & Ng, 2014. A new species, Mariaplax aspera n. sp., is described from a female collected in Lombok, Indonesia. This new species most closely resembles M. narusei Rahayu & Ng, 2014, described from Japan, but differs by its relatively narrower carapace, shorter ambulatory legs, tuberculated third maxillipeds, and shorter telson.

Paleo-drainage basin connectivity predicts evolutionary relationships across three Southeast Asian biodiversity hotspots.

Understanding factors driving diversity across biodiversity hotspots is critical for formulating conservation priorities in the face of ongoing and escalating environmental deterioration. While biodiversity hotspots encompass a small fraction of Earth's land surface, more than half the world's plants and two-thirds of terrestrial vertebrate species are endemic to these hotspots. Tropical Southeast (SE) Asia displays extraordinary species richness, encompassing four biodiversity hotspots, though disentangling multiple potential drivers of species richness is confounded by the region's dynamic geological and climatic history. Here, we use multilocus molecular genetic data from dense multispecies sampling of freshwater fishes across three biodiversity hotspots, to test the effect of Quaternary climate change and resulting drainage rearrangements on aquatic faunal diversification. While Cenozoic geological processes have clearly shaped evolutionary history in SE Asian halfbeak fishes, we show that paleo-drainage re-arrangements resulting from Quaternary climate change played a significant role in the spatiotemporal evolution of lowland aquatic taxa, and provide priorities for conservation efforts.

Cebudonus poppeorum, a new genus and new species of eumedonine crab (Crustacea: Decapoda: Brachyura: Pilumnidae) from the Philippines.

A new genus and new species of eumedonine crab, Cebudonus poppeorum, is described from the central Philippines. Superficially similar to Eumedonus H. Milne Edwards, 1834, Gonatonotus White, 1847, Zebrida White, 1847, Zebridonus Chia, Ng & Castro, 1995, and Tiaramedon Chia & Ng, 1998, Cebudonus n. gen. is easily characterised by possessing two long pseudorostral spines, a gently convex and unarmed dorsal carapace surface, elongated chelipeds that have the chela and merus unarmed and not cristate, elongated and slender ambulatory legs in which the merus is not cristate, a relatively narrow anterior male thoracic sternum, and a proportionately broader male abdomen. The general structure and colour pattern (with longitudinal stripes) suggests Cebudonus n. gen. is an obligate symbiont with echinoids.

The identity of the Sarawak freshwater crab Parathelphusa oxygona Nobili, 1901, with description of a new species, Parathelphusa nobilii, from Western Kalimantan, Indonesia, Borneo (Crustacea: Brachyura: Gecarcinucidae).

The identity of the common lowland freshwater crab in western Sarawak, Borneo, East Malaysia, Parathelphusa oxygona Nobili, 1901 (family Gecarcinucidae), is clarified. The species is redescribed and figured, and its taxonomy discussed. Specimens from western Kalimantan, Borneo, Indonesia, which have been referred to P. oxygona are here referred to a new species, Parathelphusa nobilii. The new species can be differentiated from congeners by its relatively more swollen branchial regions of the carapace, wider and lower external orbital tooth, relatively more slender male abdomen and a straight male first gonopod. 

A new species of Malayopotamon Bott, 1968 (Crustacea: Decapoda: Brachyura: Potamidae), a freshwater crab from northern Sumatra, Indonesia.

A new species of potamid freshwater crab, Malayopotamon weh sp. nov., is described from the island of Pulau Weh off northern Sumatra, Indonesia. The species superficially resembles three Sumatran species: M. batak Ng & Wowor, 1991, M. tobaense (Bott, 1968), and M. turgeo Ng & Tan, 1999, but can easily be distinguished by various carapace as well as gonopod characters.

A new species of troglobitic crab of the genus Stygothelphusa Ng, 1989, from Sarawak, Malaysia (Crustacea: Decapoda: Brachyura: Gecarcinucidae).

A new species of cave crab, Stygothelphusa antu new species, is described from limestone formations in Temurang, Sarawak, Malaysia. The new species is the most highly adapted to a cavericolous lifestyle among the four known species of Stygothelphusa, having a pale body pigmentation, reduced eyes and elongated pereopods. In contrast, the other three species have normal eyes that almost completely fill the orbits. The new species also differs from its congeners by a number of carapace, pereopod and gonopod characters.

Revision of the family Acidopsidae Stevcic, 2005, and the systematic position of Typhlocarcinodes Alcock, 1900, Caecopilumnus Borradaile, 1902, and Raoulia Ng, 1987, with descriptions of two new genera and five new species (Crustacea: Brachyura: Goneplacoidea).

The family Acidopsidae Stevcic, 2005, is revised; and two subfamilies are recognised. The Acidopsinae Stevcic, 2005, is characterised by the coxal male opening, a quadrate basal antennal article and vulvae arranged near the median longitudinal thoracic sternal groove. Three genera are included in the Acidopsinae: Acidops Stimpson, 1871 (with two species), Parapilumnus Kossmann, 1877 (with two species) and Crinitocinus gen. nov. (monotypic for Pilumnus alcocki Borradaile, 1902). The Raouliinae Stevcic, 2005 (= Typhlocarcinodidae Stevcic, 2005; Caecopilumnidae Stevcic, 2011), is characterised by its coxo-sternal male opening, a short basal antennal article which is distinctly wider than long and vulvae arranged submedially on thoracic sternite 6. Four genera are included in the Raouliinae: Raoulia Ng, 1987 (with five species, three of which are described as new), Caecopilumnus Borradaile, 1902 (with three species of which one is described as new), Typhlocarcinodes Alcock, 1900 (monotypic) and Thecaplax gen. nov. (for one new species). 

On the identity of Cancer urania Herbst, 1801 (Crustacea: Decapoda: Brachyura: Leucosiidae).

Cancer urania Herbst, 1801, is the type species of the leucosiid genus Coleusia Galil, 2006. Its identity has been a subject of confusion due to various taxonomical and nomenclatural issues. We redescribe the species, discuss its complex history and taxonomy, and a female syntype is designated as the lectotype of the species to clarify any lingering ambiguities concerning the type material of Cancer urania Herbst, 1801.

Two new species of freshwater crabs of the genus Sundathelphusa Bott, 1969 (Decapoda: Brachyura: Gecarcinucidae) from caves in Luzon, Philippines.

Two cave species of Sundathelphusa are described from a karst area in southern Luzon, Philippines. Both species have elongated ambulatory legs but the eyes and carapace pigmentation are well developed, indicating they are not troglobites. Sundathelphusa danae sp. nov. is superficially more similar to S. longipes (Balss, 1937) than to S. holthuisi Ng, 2010, which was described from the same locality. Sundathelphusa danae sp. nov. is distinguished from its closest congeners by its strongly convex anterolateral margin, more swollen branchial regions, possession of a complete frontal median triangle, laterally inflated subbranchial region and the more slender ambulatory legs. Sundathelphusa vienae sp. nov. is unusual among Sundathelphusa species in that its carapace is more quadrate, with the slender and almost straight male first gonopod tapered and having a pointed terminal segment. 

On two reports associated with James Wood-Mason and Alfred William Alcock published by the Indian Museum and the Indian Marine Survey between 1890 and 1891: implications for malacostracan nomenclature.

Two rare documents associated with the Indian Museum and the Indian Marine Survey for the administrative year April 1890 to March 1891 have been examined and found to have nomenclatural consequences for malacostracan crustaceans. Even though they constitute available published works according to the International Code for Zoological Nomenclature, these reports have rarely been cited. Dating these two publications is of importance as they make decapod scientific names available and, in a few instances, describe the same taxa. After searching the collections deposited in the Asian and African Room, British Library, the Administration Report of the Indian Marine for the year April 1890 to March 1891 could be dated with some degree of certainty as 25 August 1891. In contrast, dating the Indian Museum Annual Report proved more difficult because after examination of copies held by the General Library in the Natural History Museum, London, it was evident that not all of these reports were consistently published on time to meet an end of year deadline. However, the publication of volume XXII of the Indian Museum Annual Report for the year April 1890 to March 1891 appeared to be contemporary with the year printed at the bottom of the title page. As no exact date could be established with confidence, the publication date for this volume was fixed as 31 December 1891 in accordance with ICZN Art. 21.3.2. Therefore the Administration Report of the Indian Marine (published 25 August 1891) is considered to take precedence over the Indian Museum Annual Report (published 31 December 1891) and as such the names made available in the former take priority. As original copies of the Administration Report of the Indian Marine are not readily available in most libraries and few scientists have actually had access to these publications, the relevant Appendix No. XIII, in which the names of several malacostracan taxa are made available, is reproduced here. Since the appendix is not conclusively attributable to a specific author, it is considered to be written anonymously and should therefore be cited as Anonymous (1891). A number of names in Appendix No. XIII are available since they are accompanied by a brief description of the taxa they denote, and are either attributable to James Wood-Mason or remain with anonymous authorship; others are nomina nuda without a diagnosis or indication, or have been diagnosed previously in the "Natural History Notes from H.M. Indian Marine Survey Steamer Investigator". The nomenclatural implications for eight names made available in Anonymous (1891) are discussed: Glyphocrangon caeca, Glyphocrangon sculptus var. coecescens, Psalidopodidae, Psalidopus, Psalidopus mirabilis, Psathyrocaris, Psathyrocaris fragilis and Psopheticus crepitans. The nomenclatural history of various other taxa, initially denoted by unavailable names in Anonymous (1891), is also documented. The authorships of the various crustacean taxa collected by the Indian Marine Survey Steamer Investigator during the seasons 1889-1890 and 1890-1891, and published in two series of connected parts in the Annals and Magazine of Natural History, are also re-assessed and summarised. A rare document containing the list of R.I.M.S. Investigator stations for the period 1884-1913 is reproduced for the future benefit of the scientific community.