Bayesian Poisson tree processes and multispecies coalescent models shed new light on the diversification of Nawab butterflies in the Solomon Islands (Nymphalidae,Charaxinae, Polyura)

Butterflies of the genus Polyura form a widespread tropical group distributed from Pakistan to Fiji. The rare endemic Polyura epigenes Godman & Salvin, 1888 from the Solomon Islands archipelago represents a case of marked island polymorphism. We sequenced museum specimens of this species across its geographic range to study the phylogeography and genetic differentiation of populations in the archipelago. We used the Bayesian Poisson tree processes and multispecies coalescent models, to study species boundaries. We also estimated divergence times to investigate the biogeographic history of populations. Our molecular species delimitation and nuclear DNA network analyses unambiguously indicate that Malaita populations form an independent metapopulation lineage, as defined in the generalized lineage concept. This lineage, previously ranked as a subspecies, is raised to species rank under the name Polyura bicolor Turlin & Sato, 1995  stat. nov. Divergence time estimates suggest that this lineage split from its sister taxon in the late Pleistocene. At this time, the bathymetric isolation of Malaita from the rest of the archipelago probably prevented gene flow during periods of lower sea level, thereby fostering allopatric speciation. The combination of molecular species delimitation methods, morphological comparisons, and divergence time estimation is useful to study lineage diversification across intricate geographic regions.     

How many species of Paradoxurus civets are there? New insights from India and Sri Lanka

Using molecular data and morphological features, we investigated the species limits and genetic diversity among populations of the Asian palm civets of the genus Paradoxurus. Our main objectives were to determine the number of species within Paradoxurus hermaphroditus and to test the validity of the newly proposed species within Paradoxurus zeylonensis. Fragments of two mitochondrial (Cytochrome b, Control Region) and one nuclear (intron 7 of the beta fibrinogen) markers were sequenced from 128 individuals of P. hermaphroditus, P. zeylonensis and Paradoxurus jerdoni. DNA sequences were analysed using phylogenetic and haplotype network methods. Our analyses confirmed that P. hermaphroditus comprises three major clades, which should be recognized as separate species: P. hermaphroditus (Indian and Indochinese regions), Paradoxurus musangus (mainland Southeast Asia, Sumatra, Java and other small Indonesian islands) and Paradoxurus philippinensis (Mentawai Islands, Borneo and the Philippines). Furthermore, we have proposed that there are two subspecies within both P. musangus and P. philippinensis, and there might be at least two or three subspecies within P. hermaphroditus. We found a very low genetic diversity and no geographical structure within P. zeylonensis and did not find any support for splitting P. zeylonensis into several species nor subspecies. Finally, we confirmed that P. jerdoni and P. zeylonensis are sister species.     

Molecular phylogeny reveals high diversity and endemism in the limestone karst-restricted land snail genus Sophina Benson, 1859 from Myanmar (Eupulmonata: Helicarionidae), with description of four new species

Sophina is a poorly known and neglected genus due to the inaccessibility of the Salween Basin, Southern Myanmar. Taxonomic status, distribution, and phylogeny are being revised based on an integrative analysis of genitalia, radula, and molecular data. Morphological variation in shells and genitalia, together with a phylogenetic tree from concatenated data of mitochondrial and nuclear genes, revealed the existence of ten species/subspecies. Penial morphology and genetic divergence were generally consistent and useful in delimiting species, while shell characters showed little overall taxonomic utility in some species. Taxonomic placement of the previous subspecies “bensoni” shows clear distinction in both genitalia and molecular evidence, and is currently recognized as a distinct species. The nominal species “S. schistostelis” and “S. calias” possess similar genitalia and shell morphology, and molecular evidence suggested that they are sister taxa representing geographically isolated populations. Four new species are additionally described herein as S. furfuracea n. sp., S. pisinna n. sp., S. salweenica n. sp., and S. tonywhitteni n. sp. based on both morphology and molecular evidence. Phylogenetic analyses supported monophyly of Sophina, and further a split into two principal clades. These two clades showed little difference in genitalia, but more clear differences in the umbilical area and allopatric distribution in upper and lower reaches of the Gyaing River. High genetic divergence was revealed and this coincided with remarkable degree of endemism and localization with a pattern of one outcrop for one lineage. These data highlight the importance of the Salween Basin's karst ecosystems as an evolutionary and endemic biodiversity hotspot, and indicate that a focus on conservation and management in this area is urgently required.     

Diversity of North American map and sawback turtles (Testudines: Emydidae: Graptemys)

Map turtles of the genus Graptemys are native to North America, where a high degree of drainage endemism is believed to have shaped current diversity. With 14 species and one additional subspecies, Graptemys represents the most diverse genus in the family Emydidae. While some Graptemys species are characterized by pronounced morphological differences, previous phylogenetic analyses have failed yet to confirm significant levels of genetic divergence for many taxa. As a consequence, it has been debated whether Graptemys is taxonomically inflated or whether the low genetic divergence observed reflects recent radiations or ancient hybridization. In this study, we analysed three mtDNA blocks (3228 bp) as well as 12 nuclear loci (7844 bp) of 89 specimens covering all species and subspecies of Graptemys. Our analyses of the concatenated mtDNA sequences reveal that the widespread G. geographica constitutes the sister taxon of all other Graptemys species. These correspond to two clades, one comprised of all broad‐headed Graptemys species and another clade containing the narrow‐headed species. Most species of the broad‐headed clade are reciprocally monophyletic, except for G. gibbonsi and G. pearlensis, which are not differentiated. By contrast, in the narrow‐headed clade, many currently recognized species are not monophyletic and divergence is significantly less pronounced. Haplotype networks of phased nuclear loci show low genetic divergence among taxa and many shared haplotypes. Principal component analyses using coded phased nuclear DNA sequences revealed eight distinct clusters within Graptemys that partially conflict with the terminal mtDNA clades. This might be explained by male‐mediated gene flow across drainage basins and female philopatry within drainage basins. Our results support that Graptemys is taxonomically oversplit and needs to be revised.     

Assessing the taxonomic status of Osmoderma cristinae (Coleoptera: Scarabaeidae), endemic to Sicily,by genetic,morphological and pheromonal analyses

Resolving complexes of closely related and cryptic insect species can be challenging, especially when dealing with rare and protected taxa that are difficult to collect for genetic and morphological analyses. Until recently, populations of the genus Osmoderma (Scarabaeidae), widespread in Europe, were treated as a single species O. eremita (Scopoli, 1763) in spite of observed geographic variation in morphology. A previous survey using sequence data from the mtDNA cytochrome C oxidase I gene (COI) revealed the occurrence of at least two distinct lineages within this species complex: O. eremita in the west and O. barnabita Motschulsky, 1845, in the east. Interestingly, beetles confined to Sicily have been described as a distinct species, O. cristinae Sparacio, 1994, based on morphological traits. Only few Sicilian specimens were included in the former genetic analysis, and the results led to a still questionable taxonomic rank for these populations. To explore the robustness of the previous taxonomic arrangement for O. cristinae, a combination of genetic, morphological and pheromonal analyses was used. A 617‐bp fragment of the COI gene, aligned with O. cristinae and O. eremita sequences already available in GenBank, showed a clear genetic divergence between the two species (interspecific mean distance = 6.6%). Moreover, results from AFLP markers sustained the distinction of the two species. In addition, geometric morphometric analyses of the shape of male genitalia revealed a clear differentiation between the two species. Via scent analysis and field trapping, we demonstrated the production of the sex pheromone (R)‐(+)‐γ‐decalactone by males of O. cristinae, the attraction by conspecific individuals (mostly females) to this compound, and a lack of antagonistic effect of (S)‐(–)‐γ‐decalactone. The fact that O. eremita and O. eremita use the same compound for mate finding suggests that this sex pheromone has not undergone a differentiation and probably the allopatry of these two species compensates for the absence of a mechanism to avoid cross‐attraction. Our genetic and morphological data support the divergence of the two species and confirm the species status for O. cristinae, while sex pheromones are confirmed to be invariant among different species of the genus Osmoderma.     

Morphological and mitochondrial DNA variation revealed an undescribed lineage under the genus Sperata (Bagridae) in Bangladesh

Catfishes Sperata are popular, known for its taste and nutritional value, and are found naturally in wide variety of freshwaters in South Asia. The taxonomy of Sperata spp., sampled from Hakaluki Haor in Bangladesh, was re‐evaluated based on morphological variation and DNA barcoding. The collective variation in morphometric characters and mitochondrial DNA revealed an undescribed old and well‐separated lineage under the genus Sperata along with two previously known Sperata aor and Sperata seenghala in Bangladesh. Analyses of morphological traits suggested significant differentiation among Sperata species. The variation in mitochondrial DNA supported the distinct lineage and taxonomical discrimination. Sperata aor diverged earlier from the new lineage and Sperata seenghala with a divergence of 5.39 (CI: 3.91–7.19) Mya (PP > 90). Sperata seenghala and the new lineage shared a most recent common ancestry, which diverged from each other around 3.41 (CI: 2.24–4.62) Mya (PP > 90). Thus, the newly identified lineage could be a subspecies of S. seenghala or even a species under the genus Sperata. The information of the study will be useful for conservation, sustainable management and selective breeding of the putative species, including previously reported S. aor and S. seenghala in Bangladesh.     

New insights into the systematics of Malagasy mongoose‐like carnivorans (Carnivora,Eupleridae, Galidiinae) based on mitochondrial and nuclear DNA sequences

The Malagasy carnivorans (Eupleridae) comprise seven genera and up to ten species, depending on the authority, and, within the past decades, two new taxa have been described. The family is divided into two subfamilies, the Galidiinae, mongoose‐like animals, and the Euplerinae, with diverse body forms. To verify the taxonomic status of Galidiinae species, including recently described taxa, as well as some recognized subspecies, we studied intrageneric genetic variation and structure, using both mitochondrial and nuclear markers. Our results suggest the recognition of four species in the Galidiinae, rendering each genus monospecific. We propose to recognize three subspecies in Galidia elegans (G. e. dambrensis, G. e. elegans, and G. e. occidentalis), two subspecies in Mungotictis decemlineata (M. d. decemlineata and M. d. lineata), and two subspecies in Galidictis fasciata (G. f. fasciata and G. f. grandidieri, the latter was recently described as a distinct species). Our results indicate also that Salanoia durrelli should be treated as a junior synonym of Salanoia concolor. Low levels of intraspecific divergence revealed some geographical structure for the Galidiinae taxa, suggesting that environmental barriers have isolated certain populations in recent geological time. All taxa, whether at the species or subspecies level, need urgent conservation attention, particularly those with limited geographical distributions, as all are threatened by forest habitat degradation.     

Cryptic species in Pacific sipunculans (Sipuncula: Phascolosomatidae): east‐west divergence between non‐sister taxa

Cryptic diversity, i.e. diversity observable in genetic but not in morphological traits, is prevalent in marine invertebrates and presents one of the greatest obstacles to obtaining accurate estimates of species richness. Sipunculans, commonly called peanut worms, are marine annelids in which high levels of cryptic diversity have previously been documented. In this study, we use genetic identification techniques to examine divergence of two lineages of Pacific sipunculans, both known under the name Phascolosoma agassizii. One lineage is isolated to the eastern Pacific coast while the other one inhabits the western Pacific coast. These clades are reciprocally monophyletic and are not recovered as sister taxa, suggesting relatively early divergence within Phascolosoma. Furthermore, we did not find support for a genetic distinction between the western Pacific Phascolosoma agassizii agassizii and Phascolosoma agassizii kurilense, a subspecies reported from the Kuril Islands. Considering that the type locality for P. agassizii is in the Eastern Pacific, we suggest that the western clade, including the samples from the Kuril islands, represent a new, undescribed species.     

Phylogeography of Phrynocephalus erythrurus from the Qiangtang Plateau of the Tibetan Plateau

Phrynocephalus erythrurus of the Qiangtang Plateau occupies the highest regions of any reptile on earth. Here, we report mitochondrial DNA haplotypes sampled throughout the distribution of P. erythrurus and analyze patterns of genetic divergence among populations. The species diverged into two major lineages/subspecies at 3.67 mya corresponding to the Northern and Southern Qiangtang Plateau. The Northern Qiangtang lineage diverged into two subpopulations at 2.76 mya separated by the Beilu River Region and Wulanwula Mountains. Haplotypes from the southern Qiangtang lineage diverged 0.98 mya as a star-shaped pattern. Analyses of molecular variance indicated that most of the observed genetic variation occurred among populations/regions implying long-term interruptions to gene flow. There was no evidence of sudden recent range expansions within any of the clades/lineages. NCPA infers allopatric fragmentation and restricted gene flow as the most likely mechanisms of population differentiation. Our results also indicate the presence of at least three refugia since the Hongya glaciation. Mountain movement and glaciations since mid-Pliocene are considered to have shaped phylogenetic patterns of P. erythrurus. P. erythrurus parva is suggested as a valid subspecies of P. erythrurus. Using four calibration points, we estimate an evolutionary rate of 0.762% divergence per lineage per million years for a mitochondrial genomic segment comprising the genes encoding ND2, tRNA^Trp and tRNA^Ala.     

Temperature,energy metabolism,and adaptive divergence in two oyster subspecies

Comparisons of related species that have diverse spatial distributions provide an efficient way to investigate adaptive evolution in face of increasing global warming. The oyster subjected to high environmental selections is a model species as sessile marine invertebrate. This study aimed to detect the adaptive divergence of energy metabolism in two oyster subspecies from the genus Crassostrea—C. gigas gigas and C. gigas angulata—which are broadly distributed along the northern and southern coasts of China, respectively. We examined the effects of acute thermal stress on energy metabolism in two oyster subspecies after being common gardened for one generation in identical conditions. Thermal responses were assessed by incorporating physiological, molecular, and genomic approaches. Southern oysters exhibited higher fluctuations in metabolic rate, activities of key energetic enzymes, and levels of thermally induced gene expression than northern oysters. For genes involved in energy metabolism, the former displayed higher basal levels of gene expression and a more pronounced downregulation of thermally induced expression, while the later exhibited lower basal levels and a less pronounced downregulation of gene expression. Contrary expression pattern was observed in oxidative stress gene. Besides, energy metabolic tradeoffs were detected in both subspecies. Furthermore, the genetic divergence of a nonsynonymous SNP (SOD‐132) and five synonymous SNPs in other genes was identified and validated in these two subspecies, which possibly affects downstream functions and explains the aforementioned phenotypic variations. Our study demonstrates that differentiations in energy metabolism underlie the plasticity of adaptive divergence in two oyster subspecies and suggest C. gigas angulata with moderate phenotypic plasticity has higher adaptive potential to cope with exacerbated global warming.     

Phylogeny and biogeography of Muusoctopus (Cephalopoda: Enteroctopodidae)

Deep‐sea octopuses of the genus Muusoctopus are thought to have originated in the Pacific Northern Hemisphere and then diversified throughout the Pacific and into the rest of the World Ocean. However, this hypothesis was inferred only from molecular divergence times. Here, the ancestral distribution and dispersal routes are estimated by Bayesian analysis based on a new phylogeny including 38 specimens from the south‐eastern Pacific Ocean. Morphological data and molecular sequences of three mitochondrial genes (16S rRNA, COI and COIII) are presented. The morphological data confirm that specimens newly acquired from off the coast of Chile comprise two species: Muusoctopus longibrachus and the poorly described species, Muusoctopus eicomar. The latter is here redescribed and is clearly distinguished from M. longibrachus and other closely related species in the region. A gene tree was built using Bayesian analysis to infer the phylogenetic position of these species within the species group, revealing that a large genetic distance separates the two sympatric Chilean species. M. longibrachus is confirmed as the sister species of Muusooctopus eureka from the Falkland Islands; while M. eicomar is a sister species of Muusoctopus yaquinae from the North Pacific, most closely related to the amphi‐Atlantic species Muusoctopus januarii. Molecular divergence times and ancestral distribution analyses suggest that genus Muusoctopus may have originated in the North Atlantic: one lineage dispersed directly southward to the Magellan region and another dispersed southward along the Eastern Pacific to the Southern Ocean and Antarctica. The Muusoctopus species in the Southern Hemisphere have different phylogenetic origins and represent independent invasions of this region.     

A taxonomic revision and species delimitation of the genus Purpuraria Enderlein, 1929 (Orthoptera: Pamphagidae) using an integrative approach

Recent studies on the endemic Canarian genus Purpuraria have shown that the taxonomy of its only recognized species (P. erna) is probably erroneous. In this study, an integrative revision of the genus is performed, based on a large number of specimens and geographical sampling. As a result, (1) the diagnostic characters at the genus level are re‐described, (2) Purpuraria magna n. sp. based on morphological, morphometric and genetic data is described and (3) the taxonomic status of a formerly described subspecies is clarified. Intraspecific and interspecific morphometric differences have been found, indicating that the genus is undergoing a process of morphological diversification. Nevertheless, the possibility of interspecific mating between individuals of the two species is suggested, because no significant differences have been found between their respective calling songs. Genetic analyses using mitochondrial and nuclear DNA sequences suggest that P. erna and P. magna are recent species with evidences of secondary contact episodes in the past.     

Molecular phylogeny and divergence time estimation of Cosmodela (Coleoptera: Carabidae: Cicindelinae) tiger beetle species from Southeast Asia

Cosmodela Rivalier, 1961, represents a genus of tiger beetles that currently contains 13 described species widely distributed across Southeast Asia. A phylogenetic analysis based on the mitochondrial DNA fragments 16S and COI and the nuclear marker wingless and a phylogeographic analysis using a COI fragment were carried out on two subspecies of Cosmodela aurulenta (C. a. juxtata and C. a. aurulenta). The results support the hypothesis that these two subspecies are significantly different to be considered as separate species that diverged during the Pleistocene. TAXONDNA analysis was used to investigate the capability of the COI region as a marker for discriminating both entities and to quantify intra‐ and intertaxa genetic variation. The minimum distance between C. aurulenta and C. juxtata was 2.7837%, and no overlap of intra‐ and intertaxa genetic divergence was observed. Both taxa, here considered as valid species, occur in sympatry in the Malay Peninsula, with C. aurulenta most probably originating from the area and C. juxtata a secondary colonizer that expanded southwards from the Asian mainland. Our data infer a continental origin of the Indonesian samples of C. aurulenta, and they most likely dispersed across the land bridges that emerged during glacial maxima to form Sundaland.     

Molecular phylogeny of the deep‐sea penaeid shrimp genus Parapenaeus (Crustacea: Decapoda: Dendrobranchiata)

The commercial deep‐sea penaeid shrimp genus Parapenaeus contains 15 species, three subspecies and two forms in the Indo‐West Pacific and the Atlantic. Novel nucleotide sequence data from five different genes (COI, 16S, 12S, NaK and PEPCK) were collected to estimate phylogenetic relationships and taxonomic status amongst all but one subspecies in this genus. The phylogenetic results only support two of the four species groups previously proposed for this genus and indicate an evolution direction of the genital organs from simple to complex. The present results suggest that Parapenaeus originated in the shallow waters of the West Pacific with subsequent migration to the deep sea and the Atlantic. The molecular data reveal that there was probably misidentification of females between Parapenaeus australiensis and Parapenaeus ruberoculatus, with females previously assigned as P. australiensis likely being the females of P. ruberoculatus, while material identified as P. australiensis forma nodosa being the true P. australiensis females. On the other hand, Parapenaeus longipes forma denticulata truly represents a variation of the same species, while the subspecies Parapenaeus fissuroides indicus warrants a specific rank.     

Divergence in size,but not in shape: variation in skull size and shape within Ommatotriton newts

Using a geometric morphometric approach, we explored the variation in skull size and skull shape in banded newts (genus Ommatotriton). The genus Ommatotriton is represented by two allopatric, genetically well‐defined species: Ommatotriton ophryticus and O. vittatus. Within each species, two subspecies have been recognised. The samples used in this study cover the geographical and genetic variation within each species. We found statistically significant variation in skull size between species and among populations within species. When corrected for size, there was no significant variation in shape between species. Our results indicate that the variation in skull shape within the genus Ommatotriton is almost entirely due to size‐dependent, allometric shape changes. The exception is the shape of the ventral skull in males. Males of O. ophryticus and O. vittatus significantly diverge in the shape of the ventral cranium. The ventral skull, more precisely the upper jaw and palate, is directly functionally related to feeding. In general, our results indicate that allometry is a significant factor in the morphological variation of banded newts. However, the divergence in the ventral skull shape of males indicates that sexual selection and niche partitioning may have influenced the evolution of skull shape in these newts.     

Insights into the evolutionary history of Cervus (Cervidae,tribe Cervini) based on Bayesian analysis of mitochondrial marker sequences,with first indications for a new species

Molecular phylogeny and evolutionary history of Cervus, the most successful and widespread cervid genus, have been extensively addressed in Europe, fairly in eastern Asia, but scarcely in central Asia, where some populations have never been phylogenetically investigated with DNA‐based methods. Here, we applied a coalescent Bayesian approach to most Cervus taxa using complete mitochondrial cytochrome b gene and control region to provide a temporal framework for species differentiation and dispersal, with special emphasis on the central Asian populations from the Tarim Basin (C. elaphus bactrianus, C. elaphus yarkandensis) and Indian Kashmir (C. elaphus hanglu) aiming at assessing their phylogenetic and phylogeographic patterns. Red deer (C. elaphus), wapiti (C. canadensis) and sika deer (C. nippon) are confirmed as highly differentiated taxa, with genetic distances, divergence times and phylogenetic positions compatible with the rank of species. Similarly, the red deer of the Tarim group, hitherto considered as subspecies of C. elaphus, showed a comparable pattern of genetic distinction in the phylogeny and, according to our results, are thus worthy of being raised to the species level. The systematic position of the endangered red deer from Indian Kashmir is assessed here for the first time, and implications for its conservation are also outlined. Based on phylogeny and divergence time estimates, we propose a novel evolutionary pattern for the genus Cervus during the Mio/Pliocene, in the light of palaeo‐climatological information.     

Systematics and evolution of the libyan jird based on molecular and morphometric data

The libyan jird is one of the most widely distributed species among wild rodents, with its range extending from Morocco to China. Fifteen subspecies were described but their validity and the phylogenetic relationships among them are uncertain. Based on a comprehensive sampling, this study aims to define subspecies limits within Meriones libycus and to discuss the factors driving subspecific diversification. We used an integrative approach combining molecular (Cytochrome b and Cytochrome Oxidase Subunit 1 genes) and geometric morphometric data. Genetic data allowed us to identify three allopatric lineages within M. libycus: Western lineage in North Africa, Central lineage in Saudi Arabia, Jordan, and Syria, and Eastern lineage in Iran, Afghanistan, and China. These three lineages can also be differentiated based on skull morphology. Our results support the existence of at least three subspecies within the libyan jird: Meriones libycus libycus, M. l. syrius, and Meriones libycus erythrourus. Based on our divergence time estimates, all divergence events within M. libycus probably occurred during the Pleistocene, after 1.597 Ma. Quaternary climate fluctuations in the Sinai Peninsula explain the differentiation between the African M. l. libycus and the Levant-Arabian M. l. syrius. The differentiation of M. l. syrius with respect to the eastern M. l. erythrourus is putatively linked to the climatic fluctuations and tectonic activity of the Zagros Mountains and/or the Mesopotamia Plain of Iraq during the Pleistocene.     

Genetic isolation in an endemic African habitat specialist

The Chestnut‐banded Plover Charadrius pallidus is a Near‐Threatened shorebird species endemic to mainland Africa. We examined levels of genetic differentiation between its two morphologically and geographically distinct subspecies, C. p. pallidus in southern Africa (population size 11 000–16 000) and C. p. venustus in eastern Africa (population size 6500). In contrast to other plover species that maintain genetic connectivity over thousands of kilometres across continental Africa, we found profound genetic differences between remote sampling sites. Phylogenetic network analysis based on four nuclear and two mitochondrial gene regions, and population genetic structure analyses based on 11 microsatellite loci, indicated strong genetic divergence, with 2.36% mitochondrial sequence divergence between individuals sampled in Namibia (southern Africa) and those of Kenya and Tanzania (eastern Africa). This distinction between southern and eastern African populations was also supported by highly distinct genetic clusters based on microsatellite markers (global F_ST = 0.309,  = 0.510, D = 0.182). Behavioural factors that may promote genetic differentiation in this species include habitat specialization, monogamous mating behaviour and sedentariness. Reliance on an extremely small number of saline lakes for breeding and limited dispersal between populations are likely to promote reproductive and genetic isolation between eastern and southern Africa. We suggest that the two Chestnut‐banded Plover subspecies may warrant elevation to full species status. To assess this distinction fully, additional sample collection will be needed, with analysis of genetic and phenotypic traits from across the species’ entire breeding range.