Coral reefs as drivers of cladogenesis: expanding coral reefs, cryptic extinction events, and the development of biodiversity hotspots

Diversification rates within four conspicuous coral reef fish families (Labridae, Chaetodontidae, Pomacentridae and Apogonidae) were estimated using Bayesian inference. Lineage through time plots revealed a possible late Eocene/early Oligocene cryptic extinction event coinciding with the collapse of the ancestral Tethyan/Arabian hotspot. Rates of diversification analysis revealed elevated cladogenesis in all families in the Oligocene/Miocene. Throughout the Miocene, lineages with a high percentage of coral reef-associated taxa display significantly higher net diversification rates than expected. The development of a complex mosaic of reef habitats in the Indo-Australian Archipelago (IAA) during the Oligocene/Miocene appears to have been a significant driver of cladogenesis. Patterns of diversification suggest that coral reefs acted as a refuge from high extinction, as reef taxa are able to sustain diversification at high extinction rates. The IAA appears to support both cladogenesis and survival in associated lineages, laying the foundation for the recent IAA marine biodiversity hotspot.     

Mosaics in the mangroves: allopatric diversification of tree‐climbing mudwhelks (Gastropoda: Potamididae: Cerithidea) in the Indo‐West Pacific

The Indo‐Australian Archipelago (IAA) is the richest area of biodiversity in the marine realm, yet the processes that generate and maintain this diversity are poorly understood and have hardly been studied in the mangrove biotope. Cerithidea is a genus of marine and brackish‐water snails restricted to mangrove habitats in the Indo‐West Pacific, and its species are believed to have a short pelagic larval life. Using molecular and morphological techniques, we demonstrate the existence of 15 species, reconstruct their phylogeny and plot their geographical ranges. Sister species show a pattern of narrowly allopatric ranges across the IAA, with overlap only between clades that show evidence of ecological differentiation. These allopatric mosaic distributions suggest that speciation may have been driven by isolation during low sea‐level stands, during episodes preceding the Plio‐Pleistocene glaciations. The Makassar Strait forms a biogeographical barrier hindering eastward dispersal, corresponding to part of Wallace's Line in the terrestrial realm. Areas of maximum diversity of mangrove plants and their associated molluscs do not coincide closely. © 2013 The Natural History Museum. Biological Journal of the Linnean Society © 2013 The Linnean Society of London, 2013, 110 , 564–580.     

The genus Myrmarachne (Araneae,Salticidae) in?Flores,Indonesia

Two new species of the genus Myrmarachne are described (Myrmarachne acutidens sp. n., Myrmarachne epigealis sp. n.), and Myrmarachne macrognatha and Myrmarachne melanocephala are redescribed from Flores specimens. The females of Myrmarachne macrognatha are recorded for the first time.     

Taxonomic revision of shrews of the genus Crociduras from the Sunda Shelf and Sulawesi with description of two new species (Mammalia: Soricidae)

The skulls of 387 shrews of the genus Crocidura sampled in peninsular Malaysia, Sumatra, Borneo, Java and Sulawesi were submitted to principal component and stepwise discriminant analyses. These analyses helped to delineate morphological taxa in this species-rich genus of mammals. Most morphologic groups could be attributed to described species, except one taxon from Sumatra and one from Sulawesi, which are described and named as new. Most of the 21 species recognized in this paper are endemic to one major island. Although Sulawesi has never been connected to the mainland, it supports at least six species, followed by Sumatra (5–6 species), Java and the Malay Peninsula (4 spp) and Borneo (3 spp). C. monticola is apparently the only widespread species whose distribution range covers the entire Malay Archipelago except the Philippines and Sulawesi. In contrast, the continental C. fuliginosa enters only marginally into the Sunda Shelf: its southernmost record is on the Malay Peninsula. This interpretation is completely different from the classical view that C. fuliginosa is a cosmopolitan species occupying the whole of Southeast Asia. Identification keys, tables of measurements and discriminant functions provided in this work may aid in identification of the various species and subspecies of Crocidura living in the Malaya Archipelago.     

Endemism and evolution in the Coral Triangle: a call for clarity

In a recent paper (Bellwood & Meyer, Journal of Biogeography , 2009, 36 , 569–576), we critically evaluated the utility of marine endemics for marking the geographical origins of species. In reply, Briggs (2009) identified two issues that needed clarification: (1) whether endemics are assumed to mark the geographical origins of species or areas of exceptionally high rates of origination, and (2) whether our evaluation of the role of endemics disproves the centre of origin hypothesis. Of these two issues, the first can be clearly resolved by recourse to the original literature that explicitly states that it has been assumed that endemics do indeed mark the probable sites of origin of species. The second is equally clear: our evidence does not and can not disprove the centre of origin theory. We suggest, however, that the current data, and endemics in particular, provide limited support for centre of origin theories and that they are more consistent with some centre of accumulation theories. The Indo-Australian Archipelago (IAA; Coral Triangle) therefore appears to be an area where species persist, a centre of survival, regardless of the site of origin of species.     

Previously undocumented diversity and abundance of cryptic species: a phylogenetic analysis of Indo-Pacific Arminidae Rafinesque, 1814 (Mollusca: Nudibranchia) with descriptions of 20 new species of Dermatobranchus

The phylogenetic relationships amongst the Arminidae were analysed based upon morphological characters of 58 presently described species or nudibranchs, including 35 previously described Arminidae and 20 new species of Dermatobranchus. From the literature review and anatomical examinations, 43 characters were considered for 78 taxa. These characters were polarized using Berthella canariensis as the outgroup taxon and the type species of several other genera identified from recent publications. The resulting phylogeny supports the monophyly of Arminidae, Dermatobranchus, Doridina, and Proctonotidae. The paraphyly of the Arminina is further demonstrated in this study. Two previously described, but poorly known, species of Indo-Pacific Armina are redescribed, Armina magnaBaba, 1955 and Armina paucifoliataBaba, 1955. The anatomy and taxonomic status of nine previously described species of Dermatobranchus were examined in this study. The anatomy of Dermatobranchus pustulosus (van Hasselt, 1824) has been overlooked since Bergh (1888) illustrated the radula of van Hasselt's specimen. It is redescribed and its range is extended to several new localities in the western Pacific. Dermatobranchus pulcherrimus Miller & Willan, 1986 is considered here as a new synonym of Dermatobranchus rubidus (Gould, 1852). The following 20 species of Dermatobranchus are new and are described in the present paper: Dermatobranchus albineus sp. nov., Dermatobranchus arminus sp. nov., Dermatobranchus caesitius sp. nov., Dermatobranchus caeruleomaculatus sp. nov., Dermatobranchus cymatilis sp. nov., Dermatobranchus dendonephthyphagus sp. nov., Dermatobranchus diagonalis sp. nov., Dermatobranchus earlei sp. nov., Dermatobranchus fasciatus sp. nov., Dermatobranchus funiculus sp. nov., Dermatobranchus kalyptos sp. nov., Dermatobranchus kokonas sp. nov., Dermatobranchus leoni sp. nov., Dermatobranchus microphallus sp. nov., Dermatobranchus oculus sp. nov., Dermatobranchus phyllodes sp. nov., Dermatobranchus piperoides sp. nov., Dermatobranchus rodmani sp. nov., Dermatobranchus semilunus sp. nov., and Dermatobranchus tuberculatus sp. nov. Eighteen of these new taxa are found in the Indo-Pacific tropics and two are found in temperate South Africa, D. albineus and D. arminus. Unique combinations of morphological characters distinguish these as new species of Dermatobranchus. Several species that are externally similar have radically divergent internal morphology, are members of different clades of Dermatobranchus, and represent cryptic species. Especially important is the radular morphology, which shows remarkable diversity of form, probably related directly to the diversification of feeding of members of this clade on various octocorals.     

A new genus of rodent from Wallacea (Rodentia: Muridae: Murinae: Rattini), and its implication for biogeography and Indo‐Pacific Rattini systematics

We describe Halmaheramys bokimekot Fabre, Pagès, Musser, Fitriana, Semiadi & Helgen gen. et sp. nov. , a new genus and species of murine rodent from the North Moluccas, and study its phylogenetic placement using both molecular and morphological data. We generated a densely sampled mitochondrial and nuclear DNA data set that included most genera of Indo‐Pacific Murinae, and used probabilistic methodologies to infer their phylogenetic relationships. To reconstruct their biogeographical history, we first dated the topology and then used a Lagrange analysis to infer ancestral geographic areas. Finally, we combined the ancestral area reconstructions with temporal information to compare patterns of murine colonization among Indo‐Pacific archipelagos. We provide a new and comprehensive molecular phylogenetic reconstruction for Indo‐Pacific Murinae, with a focus on the Rattus division. Using previous results and those presented in this study, we define a new Indo‐Pacific group within the Rattus division, composed of Bullimus, Bunomys, Paruromys, Halmaheramys, Sundamys, and Taeromys. Our phylogenetic reconstructions revealed a relatively recent diversification from the Middle Miocene to Plio‐Pleistocene associated with several major dispersal events. We identified two independent Indo‐Pacific dispersal events from both western and eastern Indo‐Pacific archipelagos to the isolated island of Halmahera, which led to the speciations of H. bokimekot gen. et sp. nov. and Rattus morotaiensis Kellogg, 1945. We propose that a Middle Miocene collision between the Halmahera and Sangihe arcs may have been responsible for the arrival of the ancestor of Halmaheramys to eastern Wallacea. Halmaheramys bokimekot gen. et sp. nov. is described in detail, and its systematics and biogeography are documented and illustrated. © 2013 The Linnean Society of London     

How Charles Darwin received Wallace's Ternate paper 15 days earlier than he claimed: a comment on van Wyhe and Rookmaaker (2012)

Van Wyhe and Rookmaaker (2012) postulate a set of events to support their claim that Wallace's ‘evolution’ letter, posted at Ternate in the Moluccas in the spring of 1858, arrived at Darwin's home on 18 June 1858. If their claim were to be proven, then evidence that Darwin probably received Wallace's letter 2 weeks earlier than he ever admitted would clearly be erroneous, and any charges that he plagiarized the ideas of Wallace from that letter would be shown to be wrong. Here, evidence against this interpretation is presented and it is argued that the letter did indeed arrive in the port of Southampton on 2 June 1858 and would have been at Darwin's home near London the following day. If this were true, then the 66 new pages of material on aspects of Divergence that Darwin entered into his ‘big’ species book in the weeks before admitting he had received the letter could be interpreted as an attempt to present Wallace's ideas as his own. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 472–477.     

Sperm ultrastructure in Hemidonax pictus (Hemidonacidae, Bivalvia, Mollusca): comparison with other heterodonts, especially Cardiidae, Donacidae and Crassatelloidea

The systematic position and affinities of the marine bivalve genus Hemidonax (Heterodonta, Veneroida) are investigated using comparative sperm ultrastructure, with particular focus on the various groups to which this genus has been assigned [Donacidae (Tellinoidea), Cardiidae (Cardioidea) and Crassatellidae (Crassatelloidea)]. Ultrastructural examination (using transmission electron microscopy) reveals that Hemidonax pictus produces sperm of the aquasperm type, with a short, rounded-conical acrosomal vesicle, a short, barrel-shaped nucleus, a short midpiece (composed of two centrioles and four surrounding mitochondria) and a flagellum containing a conventional 9 + 2 pattern axoneme. The acrosomal vesicle exhibits a wedge-shaped, highly electron-dense, basal ring component, and less dense anterior component (including a thin, electron-lucent layer apically, which may prove to be a useful apomorphy for Hemidonax ). A loose, granular deposit of subacrosomal material is located within a narrow invagination traversing most of the length of the vesicle. Comparison with sperm of other heterodont bivalves shows no close connection between Hemidonax and the Donacidae (Tellinoidea) or with the Crassatellidae (or other crassatelloideans). Although certain Veneridae (Veneroidea) and Cardiidae (Cardioidea, especially Fragum ) show much better conformity in sperm morphology to that observed in Hemidonax , no complete match could be found among studied taxa. We conclude that Hemidonax should be retained in its own, previously introduced family Hemidonacidae, and the latter be placed incertae sedis within the Euheterodonta.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 153 , 325–347.     

Phylogeny of magpie‐robins and shamas (Aves: Turdidae: Copsychus and Trichixos): implications for island biogeography in Southeast Asia

Aim Magpie‐robins and shamas are forest and woodland birds of south Asia. There are two genera: Trichixos for the monotypic T. pyrrhopygus, and Copsychus for other species. Two species are widespread, whereas the others are restricted to specific islands. Endemicity is highest in the Philippines. Using phylogenetic methods, we examined how this group came to its unusual distribution. Location Mainland Asia from India to southern China, and islands from Madagascar to the Philippines. Particular emphasis is placed on the Greater Sundas and Philippines. Methods The phylogeny was estimated from DNA sequences of 14 ingroup taxa representing all nine currently recognized Copsychus and Trichixos species. The entire mitochondrial ND2 gene and portions of nuclear myoglobin intron 2 (Myo2) and transforming growth factor beta 2 intron 5 (TGFβ2‐5) were sequenced for all but two species. The phylogeny was reconstructed using maximum likelihood and Bayesian methods. The timing of divergence events was estimated using a relaxed molecular clock approach, and ancestral areas were examined using stochastic modelling. Results The group comprises three main clades corresponding to ecological types: Trichixos, a primary‐forest specialist; Copsychus magpie‐robins, open‐woodland and coastal species; and Copsychus shamas, thick‐forest species. Trichixos appears to be sister to the magpie‐robins, rendering Copsychus polyphyletic. The dating of phylogenetic nodes was too ambiguous to provide substantial insight into specific geographical events responsible for divergence within the group. Some patterns are nevertheless clear. Copsychus shamas reached the Philippines, probably in two separate invasions, and split into endemic species. Copsychus malabaricus and C. saularis expanded widely in the Greater Sundas and mainland Southeast Asia without species‐level diversification. Main conclusions Magpie‐robins are excellent dispersers and have diversified into distinct species only on isolated oceanic islands. Trichixos, a poor disperser, is restricted to mature forests of the Malay Peninsula, Sumatra and Borneo. Copsychus shamas are intermediate in habitat preference and dispersal capabilities. Their endemism in the Philippines may be attributed to early colonization and specialization to interior forests. In the Greater Sundas, C. malabaricus and C. saularis populations split and came together on Borneo to form two separate subspecies (of each species), which now hybridize.