Cryptic diversity in flathead fishes (Scorpaeniformes: Platycephalidae) across the Indo‐West Pacific uncovered by DNA barcoding

Identification of taxonomical units underpins most biological endeavours ranging from accurate biodiversity estimates to the effective management of sustainably harvested, protected or endangered species. Successful species identification is now frequently based on a combination of approaches including morphometrics and DNA markers. Sequencing of the mitochondrial COI gene is an established methodology with an international campaign directed at barcoding all fishes. We employed COI sequencing alongside traditional taxonomic identification methods and uncovered instances of deep intraspecific genetic divergences among flathead species. Sixty‐five operational taxonomic units (OTUs) were observed across the Indo‐West Pacific from just 48 currently recognized species. The most comprehensively sampled taxon, Platycephalus indicus, exhibited the highest levels of genetic diversity with eight lineages separated by up to 16.37% genetic distance. Our results clearly indicate a thorough reappraisal of the current taxonomy of P. indicus (and its three junior synonyms) is warranted in conjunction with detailed taxonomic work on the other additional Platycephalidae OTUs detected by DNA barcoding.     

Phylogeography of the Indo‐West Pacific maskrays (Dasyatidae,Neotrygon): a complex example of chondrichthyan radiation in the Cenozoic

Maskrays of the genus Neotrygon (Dasyatidae) have dispersed widely in the Indo‐West Pacific being represented largely by an assemblage of narrow‐ranging coastal endemics. Phylogenetic reconstruction methods reproduced nearly identical and statistically robust topologies supporting the monophyly of the genus Neotrygon within the family Dasyatidae, the genus Taeniura being consistently basal to Neotrygon, and Dasyatis being polyphyletic to the genera Taeniurops and Pteroplatytrygon. The Neotrygon kuhlii complex, once considered to be an assemblage of color variants of the same biological species, is the most derived and widely dispersed subgroup of the genus. Mitochondrial (COI, 16S) and nuclear (RAG1) phylogenies used in synergy with molecular dating identified paleoclimatic fluctuations responsible for periods of vicariance and dispersal promoting population fragmentation and speciation in Neotrygon. Signatures of population differentiation exist in N. ningalooensis and N. annotata, yet a large‐scale geological event, such as the collision between the Australian and Eurasian Plates, coupled with subsequent sea‐level falls, appears to have separated a once homogeneous population of the ancestral form of N. kuhlii into southern Indian Ocean and northern Pacific taxa some 4–16 million years ago. Repeated climatic oscillations, and the subsequent establishment of land and shallow sea connections within and between Australia and parts of the Indo‐Malay Archipelago, have both promoted speciation and established zones of secondary contact within the Indian and Pacific Ocean basins.     

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.     

Origins of species richness in the Indo‐Malay‐Philippine biodiversity hotspot: evidence for the centre of overlap hypothesis

The Indo‐Malay‐Philippine (IMP) biodiversity hotspot, bounded by the Philippines, the Malay Peninsula and New Guinea, is the epicentre of marine biodiversity. Hypotheses to explain the source of the incredible number of species found there include the centre of overlap hypothesis, which proposes that in this region the distinct faunas of the Pacific and Indian Oceans overlap. Here we review the biogeographical evidence in support of this hypothesis. We examined tropical reef fish distributions, paying particular attention to sister species pairs that overlap in the IMP hotspot. We also review phylogeographical studies of wide‐ranging species for evidence of lineage divergence and overlap in the IMP region. Our synthesis shows that a pattern of isolation between the Pacific and the Indian Ocean faunas is evident across a wide range of taxa. The occurrence of sister species, with one member in each ocean, indicates that the mechanism(s) of isolation has been in effect since at least the Miocene, while phylogeographical studies indicate more recent divergences in the Pleistocene. Divergence in isolation followed by population expansion has led to an overlap of closely related taxa or genetic lineages in the hotspot, contributing to diversity and species richness in the region. These findings are consistent with the centre of overlap hypothesis and highlight the importance of this process in generating biodiversity within the IMP.     

A multigene molecular assessment of cryptic biodiversity in the iconic freshwater blackfishes (Teleostei: Percichthyidae: Gadopsis) of south‐eastern Australia

Freshwater biodiversity is under ever increasing threat from human activities, and its conservation and management require a sound knowledge of species‐level taxonomy. Cryptic biodiversity is a common feature for aquatic systems, particularly in Australia, where recent genetic assessments suggest that the actual number of freshwater fish species may be considerably higher than currently listed. The freshwater blackfishes (genus Gadopsis) are an iconic group in south‐eastern Australia and, in combination with their broad, naturally divided distribution and biological attributes that might limit dispersal, as well as ongoing taxonomic uncertainty, they comprise an ideal study group for assessing cryptic biodiversity. We used a multigene molecular assessment including both nuclear (51 allozyme loci; two S7 introns) and matrilineal markers (cytb) to assess species boundaries and broad genetic substructure within freshwater blackfishes. Range‐wide examination demonstrates the presence of at least six candidate species across two nominal taxa, Gadopsis marmoratus and Gadopsis bispinosus. Phylogeographical patterns often aligned to purported biogeographical provinces but occasionally reflected more restricted and unexpected relationships. We highlight key issues with taxonomy, conservation, and management for a species group in a highly modified region. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 521–540.     

Out of Australia and back again: the world‐wide historical biogeography of non‐pollinating fig wasps (Hymenoptera: Sycophaginae)

Aim Figs (Ficus, Moraceae) are exploited by rich communities of often host‐specific phytophagous wasps. Among them, gall‐inducing Sycophaginae (Hymenoptera, Chalcidoidea) may share a common history with Ficus and their mutualistic pollinators (Agaonidae). We investigate here, for the first time, the phylogeny and biogeographical history of Sycophaginae and compare the timing of radiation and dispersion of major clades with available data on Ficus and fig pollinators. Reconstructing the history of their host colonization and association over space and time is central to understanding how fig wasp communities were assembled. Location World‐wide. Methods Maximum likelihood and Bayesian analyses were conducted on 4267 bp of mitochondrial and nuclear DNA to produce a phylogeny of all genera of Sycophaginae. Two relaxed clock methods with or without rate autocorrelation were used for date estimation. Analyses of ancestral area were also conducted to investigate the geographical origin of the Sycophaginae. Results The phylogeny is well resolved and supported. Our data suggest a post‐Gondwanan origin for the Sycophaginae (50–40 Ma) and two independent out‐of‐Australia dispersal events to continental Asia. Given palaeoclimatic and palaeogeographic records, the following scenario appears the most likely. The ancestor of Idarnes+Apocryptophagus migrated to Greater India through the Ninetyeast Ridge (40–30 Ma). The ancestor of Anidarnes+Conidarnes dispersed later via Sundaland (25–20 Ma). Idarnes and Anidarnes subsequently reached the New World via the North Atlantic land bridges during the Late Oligocene Warming Event. Apocryptophagus reached Africa c. 20 Ma via the Arabic corridors and returned to Australasia following the expansion of Sundaland tropical forests (20–10 Ma). Main conclusions Sycophaginae probably invaded the fig microcosm in Australia c. 50–40 Ma after the origin of their host plant. Once associated with figs, they dispersed out of Australia and radiated together with their host fig and associated pollinator through the tropics. We recorded a good coincidence of timing between dispersal events of Sycophaginae and continental connections. Furthermore, fruit pigeons that disperse figs probably spread out of Australasia through the Indian Ocean via the Ninetyeast Ridge c. 38 Ma. Therefore, our study highlights the potential for combining molecular phylogenetics with multiple methods of dating of interacting groups to reconstruct the historical biogeography of plant–herbivore associations.     

Hidden diversity in bent‐winged bats (Chiroptera: Miniopteridae) of the Western Palaearctic and adjacent regions: implications for taxonomy

The taxonomic status of bent‐winged bats (Miniopterus) in the Western Palaearctic and adjacent regions is unclear, particularly in some areas of the eastern Mediterranean, Middle East and Arabia. To address this, we analysed an extensive collection of museum materials from all principal parts of this distribution range, i.e. North Africa, Europe and southwest Asia, using morphological (skull) and genetic approaches (mitochondrial DNA). Linear and geometric morphometric analysis of cranial and dental characteristics, together with molecular phylogeny, suggested that Miniopterus populations comprise four separate species: (1) M. schreibersii sensu strictissimo (s.str.) – occurring in Europe, coastal Anatolia, Levant, Cyprus, western Transcaucasia, and North Africa; (2) M. pallidus – occurring in inland Anatolia, Jordan, eastern Transcaucasia, Turkmenistan, Iran and southern Afghanistan (Kandahar); (3) a Miniopterus sp. – recorded from Nangarhar province in eastern Afghanistan, which we tentatively assign to M. cf. fuliginosus; and (4) a Miniopterus sp. with Afro‐tropic affinities confirmed from south‐western Arabia and Ethiopia, which we tentatively name M. cf. arenarius. The latter two species are well differentiated by skull morphology, while M. pallidus possesses very similar skull morphology to M. schreibersii. The results also suggest the existence of a possible new taxon (subspecies) within M. schreibersii s.str. inhabiting the Atlas Mountains of Morocco. © 2012 The Linnean Society of London     

Allopatry and overlap in a clade of snails from mangroves and mud flats in the Indo‐West Pacific and Mediterranean (Gastropoda: Potamididae: Cerithideopsilla)

Cerithideopsilla is a genus of potamidid snails found in high abundance on sedimentary intertidal flats and beneath mangrove trees on continental shores in the tropical and subtropical Indo‐West Pacific region and Mediterranean Sea. Taxonomic revisions have recognized four species, but recent molecular studies have hinted at a higher diversity. Here, we analyse 377 individuals sampled from across the known range and use a combination of molecular phylogenetic (mitochondrial COI and 16S rRNA, and nuclear 28S rRNA genes), statistical (generalized mixed Yule‐coalescent GMYC method) and morphological (shell form) criteria to delimit 16 species. These form four species groups, corresponding with the traditionally recognized species C. alata, C. ‘djadjariensis’ (for which the valid name is C. incisa), C. cingulata and C. conica. Distribution maps were compiled using museum specimens identified by diagnostic shell characters. In combination with the molecular phylogenetic trees, these suggest an allopatric speciation mode, with diversification centred on the East Asian coastline and northern Australia, and a pronounced gap in the ‘eastern Indonesian corridor’, an area of low oceanic productivity. There is, however, frequently geographical overlap between sister species and we suggest from several sources of evidence (e.g. presence of C. conica in isolated saline lakes 900 km from the sea) that post‐speciation transport by migratory birds has occurred. Nine of the 16 species occur between the Gulf of Tonkin and Hong Kong, so southern China is significant for both the evolution and conservation of Cerithideopsilla species. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 114 , 212–228.     

Species diversity can be overestimated by a fixed empirical threshold: insights from DNA barcoding of the genus Cletus (Hemiptera: Coreidae) and the meta‐analysis of COI data from previous phylogeographical studies

The use of genetic distances to identify species within the framework of DNA barcoding has to some extent improved the development of biodiversity studies. However, using a fixed empirical threshold to delimit species may lead to overestimating species diversity. In this study, we use a new data set of COI sequences for 366 specimens within the genus of Cletus as well as conduct an analysis on the same genetic data for collected morphologically defined species from previous phylogeographical studies, to test whether high intraspecific genetic divergences are common with the premises of comprehensive sampling. The results indicate C. graminis Hsiao & Cheng 1964 , is the same species with C. punctiger (Dallas, 1852) and should be synonymized and that the distributional record of C. pugnator (Fabricius, 1787) in China is correct. High intraspecific genetic differentiations (0%–4.35%) were found in C. punctiger. Furthermore, as to the mined data, the maximum intraspecific K2P distances of 186 species (48.44% of 384) exceed 3%, and 101 species (26.30%) can be divided into two or more clusters with a threshold of 3% in cluster analysis. If genetic distance is used to delimit species boundaries, the minimum interspecific K2P distance of the congeneric species should be considered rather than only using the fixed empirical value; otherwise, the species richness may be overestimated in some cases.     

Continental‐scale analysis of feral cat diet in Australia,prey‐switching and the risk: benefit of rabbit control

Recent analyses of geographical variation in cats’ diet across Australia have been used to highlight rabbit control as a conservation risk, on the basis that prey‐switching by cats following rabbit control is likely to threaten Australian fauna. There is no direct evidence to support that proposition. However, there is direct evidence of repeated prey‐switching due to seasonal fluctuations in uncontrolled rabbit populations, of long‐term suppression of rabbit numbers by effective rabbit control, and that reduced rabbit abundance leads to reduced cat abundance, reduced predation of native fauna and recovery of threatened prey populations. Furthermore, rabbits are a known threat to many Australian native plants and rabbit control has proven benefits for their recovery, thereby offering long‐term benefits for dependent fauna and broader ecosystem function. On the balance of evidence, rabbit control should be encouraged in Australia wherever possible, as a national conservation priority.     

Sexual maturity and estimated fecundity in female Indo‐Pacific bottlenose dolphins (Tursiops aduncus) from South Australia: Combining field observations and postmortem results

Knowledge of life history of bottlenose dolphins in Australia is limited, with no studies comparing field and postmortem data from the same region. Carcasses of 88 opportunistically collected females (1987–2015) were studied, including eight observed for up to 23 yr before death. Ovaries were weighed and number of corpora determined grossly. Nineteen mammary glands were examined histologically. Relative age was determined using developmental features and body length, estimated age by tooth incremental lines, and physical maturity by epiphyseal fusion. Age at sexual maturation was 7.17 yr (6–>14 yr) at body lengths of 191–209 cm. Physical maturation occurred at 12–17 yr, and body lengths of 195–233 cm. An Exponential model provided the best fit for age at body length, with an asymptote at 214 cm. Combined ovary weight increased between birth and sexual maturation, with significantly more corpora in the left ovary. Corpora increased with age and appeared to persist throughout life. For mature females, 95% had ≤ 11 corpora. Number of corpora was consistent with number of calves for females with known life histories. Estimated interbirth period was about 4 yr. Three females with abnormal reproductive features were either chronically diseased and/or had high heavy metal burdens.     

No need for stepping stones: Direct,joint dispersal of the lichen‐forming fungus Mastodia tessellata (Ascomycota) and its photobiont explains their bipolar distribution

Aim

The hypotheses proposed to explain the high percentage of bipolar lichens in Antarctica have never been explicitly tested. We used the strictly bipolar, coastal lichenized fungus Mastodia tessellata (Verrucariaceae, Ascomycota) and its photobionts (Prasiola, Trebouxiophyceae, Chlorophyta) as model species to discern whether this extraordinary disjunction originated from vicariance or long‐distance dispersal.

Location

Coasts of Antarctica, Tierra del Fuego (Chile), Alaska (USA) and British Columbia (Canada).

Methods

Based on a comprehensive geographical (315 specimens and 16 populations from Antarctica, Tierra del Fuego and North America) and molecular sampling (three and four loci for the fungus and algae respectively), we implemented explicit Bayesian methods to compare alternative hypotheses of speciation and migration, and performed dating analyses for the fungal and algal partner, in order to infer the timing of the colonization events and the direction of gene flow among distant, disjunct areas.

Results

Mastodia tessellata comprises two fungal species which in turn associate with three photobiont lineages along the studied distribution range. Independent estimation of divergence ages for myco‐ and photobionts indicated a middle to latest Miocene species split in the Southern Hemisphere, and a late Miocene to Pleistocene acquisition of the bipolar distribution. Comparison of migration models and genetic diversity patterns suggested an austral origin for the bipolar species.

Main conclusions

The complex evolutionary history of Mastodia tessellata s.l. can be explained by a combination of vicariant and long‐distance dispersal mechanisms. We provide novel evidence of a pre‐Pleistocene long‐term evolution of lichens in Antarctica as well as for bipolar distributions shaped by Southern to Northern Hemisphere migratory routes without the need for stepping stones.