Evolutionary history of two allopatric Terricola species (Arvicolinae, Rodentia) from molecular, morphological, and palaeontological data

To investigate the phylogenetic and phylogeographical relationships of arvicolines, we use several Western European ground voles. More particularly, our study is focused on Microtus ( Terricola ) savii and M. ( T. ) pyrenaicus . These two allopatric species are usually considered as having originated from the same ancestor, possibly M . ( T. ) mariaclaudiae . We propose molecular and morphological approaches: nucleotidic data from the mitochondrial cytochrome b and 12S rRNA genes and global morphological analyses from the first lower molar. Four other Terricola species ( multiplex , lusitanicus , duodecimcostatus , subterraneus ) were added to the data set for both analyses, and two other vole species ( Clethrionomys glareolus and Chionomys nivalis ) as outgroup to the molecular analysis, and five fossil populations to the morphological one. Palaeontological data are also widely taken into account. Both molecular and morphological analyses indicate that intra- Terricola relationships reflect the present-day geographical distribution of our data set species. Our results show that M. ( T. ) savii and M. ( T. ) pyrenaicus are from separate speciation events leading to two different biogeographical groups, respectively the Alpine–Italian group and the French–Iberian group, the latter being much more homogeneous. These speciation events could be related to Quaternary climatic changes, which induced southward migration, leading first to M. ( T. ) savii and second to M. ( T. ) pyrenaicus . The classical hypothesis of a geographical speciation for these two taxa from M. ( T. ) mariaclaudiae is invalid. However, the morphological data suggest a potential phylogenetic relationship between M. ( T. ) mariaclaudiae (ancestor) and M. ( T. ) pyrenaicus (descendant).  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 309–323.     

Cryptic variation in mole voles Ellobius (Arvicolinae,Rodentia) of Mongolia

The mole vole subgenus Ellobius is currently considered to include three species: Ellobius talpinus (distributed from SE Europe and Turkmenistan through Kazakhstan to SW Siberia), Ellobius alaicus (S Tianshan, Pamir-Alay) and Ellobius tancrei (East and West Central Asia, from the Amu-Darya to Mongolia and N China). A study focusing on the genetic variation in Ellobius from Mongolia was conducted using one mitochondrial and three nuclear markers. Two divergent allopatric lineages endemic to East Central Asia were revealed. The first lineage occurs from Dzungaria eastwards to central Mongolia and represents E. tancrei sensu stricto. The second lineage is found in East Gobi only and corresponds to a taxon described as Ellobius orientalis, which has been traditionally treated as a subspecies of E. tancrei. However, molecular and chromosome data indicate that orientalis is related not to E. tancrei but to E. talpinus, which is separated from the former by a distribution gap of ~2,000 km. The taxonomic status of the East Gobi mole vole is ambiguous, and its genetic distance from E. talpinus s. str. falls into the range characteristic for closely related vole species or semi-species. According to molecular estimates, the two taxa have been isolated since the late Middle Pleistocene. A similar divergence is observed between the East and West Central Asian lineages of E. tancrei. E. alaicus is placed as sister to the latter rendering E. tancrei sensu lato paraphyletic. The revealed phylogeographic pattern implies that East Central Asia was colonized by mole voles through multiple eastward dispersal events.     

Cryptic Speciation in the Genus Cryptoglena (Euglenaceae) Revealed by Nuclear and Plastid SSU and LSU rRNA Gene

The photosynthetic euglenoid genus Cryptoglena is differentiated from other euglenoid genera by having a longitudinal sulcus, one chloroplast, two large trough‐shaped paramylon plates positioned between the chloroplast and pellicle, and lack of metaboly. The genus contains only two species. To understand genetic diversity and taxonomy of Cryptoglena species, we analyzed molecular and morphological data from 25 strains. A combined data set of nuclear SSU and LSU and plastid SSU and LSU rRNA genes was analyzed using Bayesian, maximum likelihood, maximum parsimony, and distance (neighbor joining) methods. Although morphological data of all strains showed no significant species‐specific pattern, molecular data segregated the taxa into five clades, two of which represented previously known species: C. skujae and C. pigra, and three of which were designated as the new species, C. soropigra, C. similis, and C. longisulca. Each species had unique molecular signatures that could be found in the plastid SSU rRNA Helix P23_1 and LSU rRNA H2 domain. The genetic similarity of intraspecies based on nr SSU rDNA ranged from 97.8% to 100% and interspecies ranged from 95.3% to 98.9%. Therefore, we propose three new species based on specific molecular signatures and gene divergence of the nr SSU rDNA sequences.     

Out of Africa? Phylogenetic relationships between Falco biarmicus and the other hierofalcons (Aves: Falconidae)

The phylogeographic history of the lanner falcon ( Falco biarmicus ) and the phylogenetic relationships among hierofalcons ( F. biarmicus , Falco cherrug , Falco jugger and Falco rusticolus ) were investigated using mitochondrial (mt) DNA sequences. Of the two non-coding mt sections tested, the control region (CR) appeared more suitable as phylogenetic marker sequence compared with the pseudo control region (ΨCR). For the comprehensive analysis samples from a broad geographic range representing all four hierofalcon species and their currently recognized subspecies were included. Moreover, samples of Falco mexicanus were analysed to elucidate its phylogenetic relationships to the hierofalcons. The sequence data indicate that this species is more closely related to Falco peregrinus than to the hierofalcons. In the DNA-based trees and in the maximum parsimony network all hierofalcons appear closely related and none of the species represents a monophyletic group. The close relationships among haplotypes suggest that the hierofalcon complex is an assemblage of morphospecies not yet differentiated in the genetic markers used in the present study and that the radiation of the four hierofalcon species took place rather recently. Based on the high intraspecific diversity found within F. biarmicus we assume an African origin of the hierofalcon complex. The observed pattern of haplotype distribution in the extant species may be due to incomplete lineage sorting of ancestral polymorphisms, and interspecific gene flow through hybridization.     

Glacial refuges and cryptic speciation in a Southern Palearctic tiger beetle (Coleoptera: Cicindelidae)

Pleistocene glaciations had a determining role for shaping the current distribution and diversity of organisms, especially in the Palearctic region. In this work, we carry out a phylogeographic analysis of Iberian and two Eastern European populations of the tiger beetle Calomera littoralis (Fabricius, 1787) in order to infer the processes that may have affected their evolutionary history. According to our results, the genetic diversity of central Iberian C. littoralis populations is very low. The haplotype networks also suggest that these populations experienced a genetic bottleneck in the past, possibly related to the last glacial maxima, similar to that observed in other cicindelid taxa. These results highlight the remarkable dispersal capacity of this species, being able to move freely from one locality to another, despite the relatively long distances of sub-optimal habitat that separates them. The genetic data of central Iberian populations contrast with those of the Eastern European populations, with higher genetic diversity and no hints of any past bottleneck. This can be explained by the different characteristics of both (Iberian and Pontic) glacial refuges. The high degree of genetic differentiation between the three C. littoralis clades, and the inclusion of C. lunulata between them, suggests that the three analysed populations could be considered as different cryptic species. In that case, C. littoralis may correspond to a species complex that is still undergoing a process of speciation, similar to that observed in Cicindela campestris.     

Integrative taxonomy of Flatbill Flycatchers (Tyrannidae) reveals a new species from the Amazonian lowlands

Integrative taxonomic studies continue to reveal that many current polytypic species of birds are in fact constituted by two or more species and therefore have been central in uncovering ‘hidden’ or ‘cryptic’ biodiversity. The Olivaceous Flatbill (Aves: Tyrannidae: Rhynchocyclus olivaceus) currently has nine recognized subspecies distributed throughout the Neotropics, but so far, no complete phylogenetic hypothesis exists to test the validity and evolutionary relationships among them. To remedy this, we conducted a multi-character integrative taxonomic revision of the genus Rhynchocyclus, focusing on the polytypic R. olivaceus. The combination of a taxonomically dense sampled multilocus phylogeny (including three mitochondrial and two nuclear genes) with phenotypic analyses including morphological and vocal characters pointed to several taxonomic inconsistencies within R. olivaceus. The analyses strongly support that R. olivaceus is paraphyletic, with an exclusively cis-Andean clade (where the topotypic R. olivaceus is found) clustering as sister to Rhynchocyclus fulvipectus, to the exclusion of a clade grouping trans-Andean and western Amazonian populations currently placed in R. olivaceus—one of which is unnamed and fully diagnosable based on vocal and genetic characters. Consistent with the phylogenetic results, our vocal analyses identified at least four morphologically cryptic lineages within R. olivaceus that can be mutually diagnosed from each other by different loudsongs and call parameters. Therefore, we provide evidence for splitting these four groups into separate species, two of which are sympatric but not syntopic in western Amazonia, including an unnamed species described herein—Rhynchocyclus cryptus, sp. nov. urn:lsid:zoobank.org:act:2DC17190-2BDD-49EC-88E6-4CF2FC2562A3.     

Bridging the morphological and biological species concepts: studies on the Bactrocera dorsalis (Hendel) complex (Diptera: Tephritidae: Dacinae) in South-east Asia

Defining species accurately is a critical need in fundamental disciplines such as ecology and evolutionary biology and in applied arenas such as pest management. The validity of species designations depends on agreement of different methods of species diagnosis for unique biological species. The Bactrocera dorsalis complex of fruit flies provide an excellent opportunity for such a test of the congruence of different techniques (e.g. morphological, molecular, host-plant based, chemotaxonomy) used for species diagnosis. The complex contains a large number of closely-related species, is distributed over a wide geographical range in South-east Asia and considerable information has been compiled on some species. In the present study, the morphological and biological species boundaries were compared using new data from morphometric analyses of reproductive and body parts, together with a review of data on morphology, chemistry of male pheromones that are important in courtship and mating, molecular analyses, and endemic rainforest host plants. For the populations studied ( Bactrocera carambolae , Bactrocera dorsalis , Bactrocera occipitalis , Bactrocera papayae , Bactrocera philippinensis , Bactrocera kandiensis and Bactrocera invadens ) there appears to be significant congruence between the morphological and biological species boundaries.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 217–226.     

Intricate evolutionary histories in montane species: a phylogenetic window into craniodental discrimination in the Peromyscus mexicanus species group (Mammalia: Rodentia: Cricetidae)

Mountain‐associated species, which exhibit allopatric distributions associated with elevation, endemisms and complex evolutionary histories, pose challenging evolutionary scenarios in which to discern the diversification of species. The Peromyscus mexicanus mice group, distributed along mountains in southern Mexico and Central America, is morphometrically variable, a key rationale for the ongoing controversy regarding its species delimitation. Based on the recognized 15 mitochondrial lineages for the group, we analysed external and craniodental morphometric variables to test whether lineages can be differentiated morphometrically and allow for the delimitation of species. We also aimed to test the prediction that the phylogenetic structure of the morphometric data is concordant with that of the molecular information. Based on 19 craniodental measurements from 521 specimens, multivariate and discriminant analyses showed that lineages are morphometrically discernible, representing distinct phenotypes, and that overall size and mandible measurements are significant features that discriminate lineages, supporting hypotheses about differences in feeding habits between species. Also, a pattern of increasing size with elevation was observed, further supported by specific morphological differences exhibited between highland and lowland lineages inhabiting the same mountain. Our results demonstrate that P. mexicanus is both genetically and morphometrically variable, where most highland montane species are differentiated from lowland species; also, a significant correlation between mitochondrial and morphometric information is indicative of phenetic concordance, altogether in agreement with a recent taxonomic proposal for the group. We suggest that the group's intricate diversification responds to ecological diversification and adaptation to a variety of mountain habitats and Pleistocene biogeographic climatic dynamics.     

Evolutionary history of the scorpionfly Dicerapanorpa magna (Mecoptera,Panorpidae)

Climate changes can have fundamental impacts on the distributional patterns of montane species, and range shifts frequently lead to allopatric divergence followed by the establishment of secondary contact zones. Many European and North American organisms have retreated to southern refugia during glacial periods and colonized northward during postglacial periods, but little is known about the evolutionary response of cold‐adapted insects to Pleistocene climate changes in eastern Asia. The scorpionfly Dicerapanorpa magna (Chou), with cold temperate habitat preference and weak dispersal ability, provides a good model system to explore how climate changes have influenced the distribution and divergence of cold‐adapted insects in eastern Asia. This study reconstructed the demographic dynamics and evolutionary history of D. magna with phylogeographic approaches, and predicted the species’ suitable areas under the Last Glacial Maximum (LGM) and current scenarios with the ecological niche modelling analysis. The mitochondrial cytochrome c oxidase subunit I resolved three phylogenetic lineages in D. magna dating back to Pleistocene, corresponding well with the geographically isolated Qinling, Bashan and Minshan Mountains. The ecological niche modelling recovered the suitable habitats for D. magna were the Qinling and Bashan Mountains under LGM and current conditions. The three lineages of D. magna might be in a process of incipient speciation, and likely derived their current distribution from separate glacial origins, followed by vicariance and divergence.     

Taxonomic revision of the marbled skink (Cyclodina oliveri,Reptilia: Scincidae) species complex,with a description of a new species

Abstract

We have completed a taxonomic revision of the New Zealand marbled skink (Cyclodina oliveri) species complex. Morphological analyses and mitochondrial sequence data (ND2, ND4, Cytochrome b; Total 1933 bp) are used to describe a new taxon (commonly known as the “Mokohinau” skink) and redefine C. oliveri. The morphological and molecular data indicate that C. oliveri is distributed on the Poor Knights Islands, Mercury Islands and Aldermen Islands. The new species is restricted to the Mokohinau Islands, Hen and Chickens group, Little Barrier Island and Great Barrier Island. Our data demonstrate that there is no support for the separation of the Poor Knights Islands population of C. oliveri from those on the Mercury Islands and Aldermen Islands. The genetic data indicate that C. whitakeri is part of the C. oliveri species group. Divergence time estimates indicate that the C. oliveri species complex diverged during the late‐Miocene, with further divergences among island groups in C. oliveri including the origin of the new taxon during the late‐Pliocene and mid‐Pleistocene. We present a diagnostic key for Cyclodina.     

Cryptic lineage divergence in marine environments: genetic differentiation at multiple spatial and temporal scales in the widespread intertidal goby Gobiosoma bosc

The adaptive radiation of the seven‐spined gobies (Gobiidae: Gobiosomatini) represents a classic example of how ecological specialization and larval retention can drive speciation through local adaptation. However, geographically widespread and phenotypically uniform species also do occur within Gobiosomatini. This lack of phenotypic variation across large geographic areas could be due to recent colonization, widespread gene flow, or stabilizing selection acting across environmental gradients. We use a phylogeographic approach to test these alternative hypotheses in the naked goby Gobiosoma bosc, a widespread and phenotypically invariable intertidal fish found along the Atlantic Coast of North America. Using DNA sequence from 218 individuals sampled at 15 localities, we document marked intraspecific genetic structure in mitochondrial and nuclear genes at three main geographic scales: (i) between Gulf of Mexico and Atlantic Coast, (ii) between the west coast of the Florida peninsula and adjacent Gulf of Mexico across the Apalachicola Bay, and (iii) at local scales of a few hundred kilometers. Clades on either side of Florida diverged about 8 million years ago, whereas some populations along the East Cost show divergent phylogroups that have differentiated within the last 200,000 years. The absence of noticeable phenotypic or ecological differentiation among lineages suggests the role of stabilizing selection on ancestral phenotypes, together with isolation in allopatry due to reduced dispersal and restricted gene flow, as the most likely explanation for their divergence. Haplotype phylogenies and spatial patterns of genetic diversity reveal frequent population bottlenecks followed by rapid population growth, particularly along the Gulf of Mexico. The magnitude of the genetic divergence among intraspecific lineages suggests the existence of cryptic species within Gobiosoma and indicates that modes of speciation can vary among lineages within Gobiidae.     

The Caribbean slipper spurge Euphorbia tithymaloides: the first example of a ring species in plants

A ring species arises when a parental population expands around an area of unsuitable habitat in such a way that when the two fronts meet they behave as distinct species while still being connected through a series of intergrading populations. Ring species offer great possibilities for studying the forces causing species divergence (e.g. the nature of pre-zygotic or post-zygotic reproductive isolation) or helping to maintain species integrity (e.g. reinforcement). Yet, ring species are extremely rare, and have only been documented convincingly in animals. Here, we present phylogenetic analyses of two nuclear gene regions from the Caribbean slipper spurge (Euphorbia tithymaloides) species complex that provide evidence that this group forms a ring species. These data show that the species complex originated in the area where Mexico and Guatemala meet, and expanded around the Caribbean basin along two distinct fronts: one eastward through the Yucatan Peninsula and into the Greater Antilles (GA); one southeastward through northern South America and then northward to the Lesser Antilles and eastern GA. The two terminal forms co-occur in the Virgin Islands and appear to be morphologically and ecologically distinct. Thus, our results suggest that Euphorbia tithymaloides is the first compelling example of a ring species in plants.     

On the genetic diversity in the mitochondrial 12S rRNA gene of Platymantis frogs from Western New Guinea (Anura: Ceratobatrachidae)

Platymantis is a group of neobatrachian frogs that occurs from the Philippines to New Guinea – an area situated at the interface between the Australian and Asian biogeographical region that is highly fragmented by stretches of open sea. Partial sequences of the mitochondrial 12S rRNA gene are herein used to infer the relationships of species from the Indonesian part of New Guinea (Papua and West Papua Province). The phylogenetic trees reveal a deep bifurcation between the Asian and Western New Guinean clades being consistent with phylogeographic patterns observed in various other faunal groups. While most species are well differentiated in the examined locus, low interspecific genetic distances between one and three percent were observed in the New Guinean species Platymantis papuensis and P. cryptotis as well as P. pelewensis from Palau. Platymantis papuensis and P. pelewensis are geographically separated from each other by a 1100 km stretch of open sea. The minor degree of genetic differentiation between both species points to a recent event of transmarine dispersal as causation for the occurrence of P. pelewensis on Palau. The low genetic differentiation between P. cryptotis and the sympatric P. papuensis, two species that are bioacoustically and morphologically distinct, may indicate its possibly recent evolutionary origin or, alternatively, yet undetected hybridization between the two species. The same may also hold true for frogs from Yapen that exhibit calls different from the sympatric P. papuensis. Tentatively referred to as Platymantis spec., these frogs are also genetically not well differentiated. It is furthermore concluded that the partly low genetic differentiation of the New Guinean Platymantis species render this group one of the cases in which DNA barcoding would likely fail to produce reliable results.     

Cryptic species of the subgenus Morphnosoma Lutshnik (Coleoptera: Carabidae; genus Pterostichus) from Japan

Pterostichus thunbergi Morawitz and its related species of Japan are revised based on the structure of membranous parts of their genitalia for the first time, under the name of the thunbergi species group. This species group is monophyletic and is placed in the subgenus Morphnosoma Lutshnik. The monotypic subgenus Moritapterus Berlov, erected for P. thunbergi, is synonymized with Morphnosoma. Comparative study of the endophallus revealed that P. thunbergi michinoku Nakane is a junior synonym of P. habui and that four species should be recognized in this group. Three of them are sympatric with P. thunbergi and one of them, Pterostichus (Morphnosoma) robustistylis, is described as a new species. Molecular phylogeny based on the COI gene (mitochondrial [mt]DNA) supported its independence as a distinct species. The resultant trees of mtDNA and comparative study of morphology revealed that P. thunbergi is probably non‐monophyletic. In the present study we suggest the presence of further cryptic species of Morphnosoma in Japan.     

Marcusenius desertus sp. nov. (Teleostei: Mormyridae), a mormyrid fish from the Namib desert

We critically compared Marcusenius specimens from the mouth of the Cunene River on the Namibia/Angola border, a harsh desert environment on the Atlantic Ocean coast virtually devoid of aerial insects with aquatic larvae which are an important food item, with Marcusenius multisquamatus Kramer & Wink, 2013 from the escarpment region of that same river, in a relatively rich and productive subtropical savannah environment. River mouth specimens were differentiated in morphology and electric organ discharges, as determined by ANOVA/MANOVA comparisons, principal component and discriminant analyses on morphological and electrophysiological characters, and genetics, including sequences of the mitochondrial cytochrome b gene, indicating reproductive isolation. Specimens from the river mouth differed from M. multisquamatus, their closest relatives, by having a shorter snout, a smaller eye diameter, and smaller nares separation. River mouth specimens were also differentiated from other, increasingly less-close relatives, such as M. altisambesi Kramer et al., 2007 from the Okavango River, Botswana, and from M. krameri Maake et al., 2014 from the Limpopo System, South Africa. We therefore designate the new species Marcusenius desertus sp. nov. for the Cunene River mouth population.     

Intergeneric phylogenetic relationships in catfishes of the Loricariinae (Siluriformes: Loricariidae), with the description of Fonchiiloricaria nanodon: a new genus and species from Peru

Recent investigations in the upper Río Huallaga in Peru revealed the presence of an intriguing species of the Loricariinae. To characterize and place this species within the evolutionary tree of the subfamily, a molecular phylogeny of this group was inferred based on the 12S and 16S mitochondrial genes and the nuclear gene F-reticulon4. The phylogeny indicated that this distinctive species was a member of the subtribe Loricariina. Given its phylogenetic placement, and its unusual morphology, this species is described as a new genus and new species of Loricariinae: Fonchiiloricaria nanodon. This new taxon is diagnosed by usually possessing one to three premaxillary teeth that are greatly reduced; lips with globular papillae on the surface; the distal margin of lower lip bearing short, triangular filaments; the premaxilla greatly reduced; the abdomen completely covered by plates, with the plates between lateral abdominal plates small and rhombic; a caudal fin with 14 rays; the orbital notch absent; five lateral series of plates; dorsal-fin spinelet absent; preanal plate present, large and solid, and of irregular, polygonal shape, the caudal peduncle becoming more compressed posteriorly for the last seven to 10 plates.     

Rhagada revisited: on the taxonomy of species from the Kimberley and Dampierland,Western Australia (Pulmonata,Camaenidae)

The genus Rhagada is the second most diverse camaenid genus in Australia. We examined anatomical and mitochondrial characters of previously unidentified material from the Kimberley that was earmarked to potentially represent new species in recently published molecular phylogenetic studies. Our comparisons revealed that specimens from Gibbings Island (‘R. sp. Gibbings’) were morphologically and genetically most similar to Rhagada cygna from the Dampier Peninsula. Hence, ‘R. sp. Gibbings’ is considered to be identical to R. cygna. In addition, we found that R. cygna as so delimited is not clearly distinguished from the second species on the Dampier Peninsula, Rhagada bulgana. Both species differ rather subtly in anatomical and mitochondrial characters, indicating their close relationships and potentially incomplete evolutionary differentiation. Furthermore, we describe two new species based on comparative morphology and mitochondrial sequences: Rhagada worora n. sp. from the Prince Regent Reserve in the Kimberley and Rhagada karajarri n. sp. from Dampierland. The present study confirms that species in Rhagada are best identified by means of both morphological and molecular data.

http://zoobank.org/urn:lsid:zoobank.org:pub:556E1866-6F9E-4CC0-8ACF-CD56E929501F