Phylogeny of Indo‐West Pacific pontoniine shrimps (Crustacea: Decapoda: Caridea) based on multilocus analysis

The phylogenetic relationships and evolutionary processes within the subfamily Pontoniinae, a speciose group of shrimps with diverse lifestyles (free living, semi‐symbiotic and symbiotic) inhabiting the coral reefs of tropical oceans, are an interesting and undeveloped subject of study. In this work, two mitochondrial ribosomal genes (12S rRNA and 16S rRNA) and two protein‐coding nuclear genes (Histone 3 and the sodium–potassium ATPase α‐subunit) were employed to reconstruct the phylogenetic relationships of 42 genera and 101 species within Pontoniinae. Compared to previous studies, ten additional genera were shown to be monophyletic groups, and the genera Dactylonia and Periclimenaeus were shown to be paraphyletic. The shallow‐water crinoid‐associated pontoniines were divided into several groups which were mostly consistent with the morphological analysis. The studied bivalve‐associated taxa exhibited ancestries that were traceable to different lineages, and two groups could be distinguished: Anchiopontonia + Conchodytes and Anchistus. The similar situation occurred in other echinoderm‐associated pontoniines. These results suggest that pontoniines sharing the same hosts may have different evolutionary origins resulting from multiple intrusions of their hosts by morphologically plastic ancestral groups.     

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 and species of long-clawed mouse (Rodentia: Muridae) from temperate rainforests of Chile

Morphological comparisons of long-clawed mice in southern South America reveal the existence of four genera, only three of which are named. The fourth genus is described and compared with Geoxus, Chelemys and Notiomys. External, cranial and dental characters indicate that the new mouse is most closely related to Geoxus , the raton topo or mole mouse. Geoxus and the new form may be distinguished using both qualitative and quantitative characters. The incipient specializations of the new mouse for fossorial life suggest that it represents an early offshoot along the line leading to the more highly specialized Geoxus. Discovery of a new mammalian genus in Chile, where naturalists have been active for more than two centuries, indicates the importance of continued biological surveys, even in ostensibly well-studied regions. The new mouse reinforces the strong differentiation of faunas inhabiting southern beech ( Nothofagus ) forests in South America, where generic endemism of rodents and marsupials reaches 67%.     

Evolutionary systematics and biogeography of the arid habitat‐adapted rodent genus Gerbillus (Rodentia,Muridae): a mostly Plio‐Pleistocene African history

The systematics of the arid‐adapted Old World Gerbillus rodent genus has always been challenging, with many different taxonomic arrangements proposed. Beyond such taxonomic aspects, the timing and geographical pattern of the evolutionary history of this group remains largely unknown. Based on mitochondrial (cytochrome b) and nuclear (interphotoreceptor retinoid‐binding protein) sequences obtained from the specimens of 21 species, we conducted a phylogenetic analysis of the group, estimated the ages and putative ancestral ranges of its major lineages. Four major clades were clearly retrieved within Gerbillus, for which we propose a subgenus rank. We showed that the emergence of the genus dates back to the end of the Miocene, which corresponds to a period of aridification and C4 vegetation expansion in open habitats, while the four sublineages originated at the end of the Pliocene. Most subsequent diversification events occurred during the Pleistocene, a period characterized by recurrent climatic/environmental shifts with increasing aridification during the last two millions of years. Finally, we suggested that most of the Gerbillus evolutionary history took place in Africa. Only in a few instances did dispersal events from Africa to Asia give birth to extant Asian lineages, a pattern that contrasts with what has been found in many animal groups.     

Historical biogeography and molecular systematics of the Indo-Pacific genus Dascyllus (Teleostei: Pomacentridae)

The phylogeographical and systematic relationships among species in the tropical marine fish genus Dascyllus were inferred using mitochondrial DNA (mtDNA) sequence data. Although our results were generally consistent with previously published phylogenies based on both morphological and mitochondrial data, our broad taxonomic and geographical sampling design revealed novel insights into the phylogenetic history of Dascyllus that had escaped previous notice. These results include: (a) the polyphyletic nature of D. reticulatus mtDNAs, representing two divergent and geographically separated lineages, one shared with D. flavicaudus and the second forming the sister lineage of D. carneus; (b) the paraphyly of D. trimaculatus relative to the closely related D. abisella; and (c) phylogeographical structure within the widespread taxa D. aruanus and D. trimaculatus. Application of a molecular clock permits us to posit a causative role for tectonic and oceanic changes regarding some Dascyllus speciation events. Finally, we mapped body size and the presence or absence of protogynous sex change on the mtDNA tree, and tested published hypotheses regarding determinants of the evolution of mating system and protogyny in the genus. Our data rejected a model based on body size but not one based on phylogenetic inertia. The ability to change sex arose once in the ancestor to the entire genus, and was lost once in the ancestor of the D. trimaculatus complex. For taxa that are as geographically widespread as many Indo-Pacific genera, this study highlights the importance of adequate geographical sampling when inferring patterns of species diversification and life history evolution.     

Connectivity and the development of population genetic structure in Indo‐West Pacific coral reef communities

Aim To identify connectivity patterns among coral reefs of the Indo‐West Pacific. Projecting connectivity forward in time provides a framework for studying long‐term source–sink dynamics in the region, and makes it possible to evaluate the manner in which migration shapes population genetic structure at regional scales. This information is essential for addressing critical gaps in knowledge for conservation planning efforts in one of the most biologically diverse regions on earth. Location Coral reefs of the Indo‐West Pacific, ranging from 15° S to 30° N and 95° E to 140° E. Methods Individual‐based biophysical dispersal models were used in conjunction with matrix projection to identify the expected patterns of exchange between coral reefs over time. Results Present‐day oceanographic conditions lead to the transport of larvae from the South China Sea into the Coral Triangle region via the Sulu Sea, and from northern Papua New Guinea and the Solomon Islands via Halmahera. The directionality of the system leads to the expected accumulation of organisms from outlying areas into the Coral Triangle region over time, particularly in the vicinity of the Maluku Islands and eastern Sulawesi. Coral reefs in Papua New Guinea, the Sulu Archipelago and areas within the Philippines are expected to be areas of high diversity as well. Main conclusions Biophysical dispersal models, used in conjunction with matrix projection, provide an effective means of simulating connectivity structure across the Indo‐West Pacific and thereby evaluating the directionality of genetic diversity. Migration appears to have a significant influence on population genetic structure in the region. Based on present‐day ocean currents, coral reefs in the South China Sea, northern Papua New Guinea and the Solomon Islands are contributing to high levels of diversity in the Coral Triangle.     

Historical biogeography of an Indo‐Pacific passerine bird family (Pachycephalidae): different colonization patterns in the Indonesian and Melanesian archipelagos

Aim We use molecular‐based phylogenetic methods and ancestral area reconstructions to examine the systematic relationships and biogeographical history of the Indo‐Pacific passerine bird family Pachycephalidae (whistlers). Analysed within an explicit spatiotemporal framework, we elucidate distinct patterns of diversification across the Melanesian and Indonesian archipelagos and explore whether these results may be explained by regional palaeogeological events. We further assess the significance of upstream colonization and its role in species accumulation within the region. Location The Indo‐Pacific region, with an emphasis on the archipelagos on either side of the Australo‐Papuan continent. Methods We used three nuclear and two mitochondrial markers to construct a molecular phylogenetic hypothesis of the Pachycephalidae by analysing 35 of the 49 species known to belong to the family. The programs diva and Mr Bayes were used to reconstruct ancestral area relationships and to examine biogeographical relationships across the family, and beast was implemented to assess the timing of dispersal events. Results We constructed a molecular phylogenetic hypothesis for the Pachycephalidae and estimated divergence times and ancestral area relationships. Different colonization patterns are apparent for the Pachycephalidae in the Indonesian and the Melanesian archipelagos. The Indonesian archipelago was colonized numerous times, whereas one or two colonizations of the Melanesian archipelagos account for the entire diversity of that region. After initial colonization of the Melanesian archipelagos some whistler species recolonized Australia and may have commenced a second round of colonization into Melanesia. Main conclusions The contrasting dispersal patterns of whistlers in archipelagos on either side of the Australo‐Papuan continent are congruent with the arrangement and history of islands in each of the regions and demonstrate that knowledge of palaeogeography is important for an understanding of evolutionary patterns in archipelagos. We also highlight that recolonization of continents from islands may be more common than has previously been assumed.     

‘After Africa’: the evolutionary history and systematics of the genus Charaxes Ochsenheimer (Lepidoptera: Nymphalidae) in the Indo‐Pacific region

The predominantly Afrotropical genus Charaxes is represented by 31 known species outside of Africa (excluding subgenus Polyura Billberg). We explored the biogeographic history of the genus using every known non‐African species, with several African species as outgroup taxa. A phylogenetic hypothesis is proposed, based on molecular characters of the mitochondrial genes cytochrome oxidase subunit I (COI) and NADH dehydrogenase 5 (ND5), and the nuclear wingless gene. Phylogenetic analyses based on maximum parsimony and Bayesian inference of the combined dataset implies that the Indo‐Pacific Charaxes form a monophyletic assemblage, with the exception of Charaxes solon Fabricius. Eight major lineages are recognized in the Indo‐Pacific, here designated the solon (+African), elwesi, harmodius, amycus, mars, eurialus, latona, nitebis, and bernardus clades. Species group relationships are concordant with morphology and, based on the phylogeny, we present the first systematic appraisal and classification of all non‐African species. A biogeographical analysis reveals that, after the genus originated in Africa, the evolutionary history of Charaxes in the Indo‐Pacific, in particular Wallacea, may be correlated with the inferred geological and climatic history of the region. We propose that Wallacea was the area of origin of all Charaxes (excluding C. solon) occurring to the east of Wallace's [1863] Line. The earliest Indo‐Pacific lineages appear to have diverged subsequent to the initial fragmentation of a palaeo‐continent approximately 13 million years ago. Further diversification in Indo‐Pacific Charaxes appears primarily related to climatic changes during the Pliocene and possibly as recently as the Pleistocene. Although both dispersal and vicariance have played important roles in the evolution of the genus within the region, the latter has been particularly responsible for diversification of Charaxes in Wallacea. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 457–481.     

Albumin preservation in fossil bones and systematics of Malpaisomys insularis (Muridae,Rodentia), an extinct rodent of the Canary Islands

Collagen and albumin were extracted from subfossil bones of the extinct rodent Malpaisomys insularis; the radiocarbon age of the sample was at least 1.73 Ka. Electrophoretic and immunological techniques indicate the preservation of albumin while collagen is revealed as degraded fragments. Immunological comparisons between Malpaisomys albumin and albumin antisera of four extant rodents indicate that Malpaisomys is more closely related to Mus than to Acomys and Uranomys and that Cavia is the most divergent taxon studied. The branching order of the fossil and the extant rodents is discussed with respect to the relationships derived from morphological criteria.     

A new genus and species of rodent from the Brazilian Atlantic Forest (Rodentia: Cricetidae: Sigmodontinae: Oryzomyini), with comments on oryzomyine biogeography

We describe in this paper a new genus and species of cricetid rodent from the Atlantic Forest of Brazil, one of the most endangered eco‐regions of the world. The new form displays some but not all synapomorphies of the tribe Oryzomyini, but a suite of unique characteristics is also observed. This new forest rat possesses anatomical characteristics of arboreal taxa, such as very developed plantar pads, but was collected almost exclusively in pitfall traps. Phylogenetic analyses of morphological (integument, soft tissue, cranial, and dental characters) and molecular [nuclear – Interphotoreceptor retinoid binding protein (Irbp) – and mitochondrial – cytochrome b– genes] datasets using maximum likelihood and cladistic parsimony approaches corroborate the inclusion of the new taxon within oryzomyines. The analyses also place the new form as sister species to Eremoryzomys polius, an Andean rat endemic to the Maranon valley. This biogeographical pattern is unusual amongst small terrestrial vertebrates, as a review of the literature points to few other similar examples of Andean–Atlantic Forest pairings, in hylid frogs, Pionus parrots, and other sigmodontine rodents. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 357–390.     

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.     

Present and past genetic connectivity of the Indo‐Pacific tropical eel Anguilla bicolor

Aim The objective of this study was to reveal the present population structure and infer the gene‐flow history of the Indo‐Pacific tropical eel Anguilla bicolor. Location The Indo‐Pacific region. Methods The entire mitochondrial control region sequence and the genotypes at six microsatellite loci were analysed for 234 specimens collected from eight representative localities where two subspecies have been historically designated. In order to infer the population structure, genetic differentiation estimates, analysis of molecular variance and gene‐tree reconstruction were performed. The history of migration events and population growth was assessed using neutrality tests based on allelic frequency spectrum, coalescent‐based estimation of gene flow and Bayesian demographic analysis using control region sequences. Results Population structure analysis showed genetic divergence between eels from the Indian and Pacific oceans (F_ST = 0.0174–0.0251, P < 0.05 for microsatellites; Φ_ST = 0.706, P < 0.001 for control region), while no significant variation was observed within each ocean. Two mitochondrial sublineages that do not coincide with geographical regions were found in the Indian Ocean clade of a gene tree. However, these two sublineages were not differentiated at the microsatellite markers. The estimation of mitochondrial gene‐flow history suggested allopatric isolation between the Indian and Pacific oceans, and a possible secondary contact within the Indian Ocean after an initial population splitting. Bayesian demographic history reconstruction and neutrality tests indicated population growth in each ocean after the Indo‐Pacific divergence. Main conclusions Anguilla bicolor has diverged between the Indian and Pacific oceans, which is consistent with the classical subspecies designation, but is apparently genetically homogeneous in the Indian Ocean. The analysis of gene‐flow and demographic history indicated that the two mitochondrial sublineages observed in the Indian Ocean probably represent the haplotype groups of relict ancestral populations. A comparison with a sympatric congener suggested that absolute physical barriers to gene flow may not be necessary for population divergence in eels.     

Diversification of a ‘great speciator’ in the Wallacea region: differing responses of closely related resident and migratory kingfisher species (Aves: Alcedinidae: Todiramphus)

The Collared Kingfisher species complex is the most widespread of the ‘great speciator’ lineages of the Indo‐Pacific. They have shown a remarkable ability to spread and diversify. As a result of this rapid diversification, Todiramphus species are often found in secondary sympatry. In Southeast Sulawesi, Indonesia, two Todiramphus species are present, the breeding resident Collared Kingfisher Todiramphus chloris and the overwintering migratory Sacred Kingfisher Todiramphus sanctus. We investigated the effect of isolation on these closely related species by comparing their populations on mainland Sulawesi and its larger continental islands, with populations on the small, oceanic Wakatobi Islands. Within our wider analysis we provide further support for the distinctiveness of the Sulawesi Collared Kingfisher population, perhaps isolated by the deep water barrier of Wallace's line. Within Sulawesi we found that populations of Collared Kingfisher on the Wakatobi Islands had diverged from those on mainland Sulawesi, differing both in morphology and in mitochondrial DNA. In contrast, there was no divergence between Sacred Kingfisher populations in either morphology or mitochondrial DNA. We propose that a difference in habitat occupied by Collared Kingfisher populations between the mainland and continental islands vs. oceanic islands has caused this divergence. Mainland Collared Kingfishers are predominately found inland, whereas Wakatobi Collared Kingfishers are also found in coastal habitats. The larger body size of Wakatobi Collared Kingfisher populations may be a result of increased competition with predominantly coastal Sacred Kingfisher populations. The uniform nature of Sacred Kingfisher populations in this region probably reflects their consistent habitat choice (coastal mangrove) and their migratory nature. The demands of their breeding range are likely to have an even stronger selective influence than their Sulawesi wintering range, limiting their scope for divergence. These results provide insight into the adaptability of the widespread Todiramphus lineage and are evidence of the need for further taxonomic revision of Collared Kingfisher populations.