Novel molecular markers differentiate Oncorhynchus mykiss (rainbow trout and steelhead) and the O. clarki (cutthroat trout) subspecies

A suite of 26 PCR‐based markers was developed that differentiates rainbow (Oncorhynchus mykiss) and coastal cutthroat trout (O. clarki clarki). The markers also differentiated rainbow from other cutthroat trout subspecies (O. clarki), and several of the markers differentiated between cutthroat trout subspecies. This system has numerous positive attributes, including: nonlethal sampling, high species‐specificity and products that are easily identified and scored using agarose gel electrophoresis. The methodology described for developing the markers can be applied to virtually any system in which numerous markers are desired for identifying or differentiating species or subspecies.     

Phylogeny,host association and biogeographical patterns in the diverse millipede‐parasitoid genus Myriophora Brown (Diptera: Phoridae)

Myriophora is the most species‐rich group of parasitoids that attack toxic, chemically defended millipedes in the superorder Juliformia and order Polydesmida—a resource that few insect predators and parasitoids are able to exploit. Worldwide, there are an estimated 200 species of Myriophora, with the majority of the diversity centred in the Neotropical region. The phylogeny of Myriophora is unknown, biogeographical patterns are not documented, and known host associations have not been assessed in a phylogenetic context. We provide the first phylogenetic study of the genus from a data set composed of 52 taxa primarily from the Neotropical region including 10 outgroups, 40 morphological characters, and molecular data from three mitochondrial (16S, COI and ND1) and one nuclear marker (AK). We find that Myriophora dispersed from the New World to the Old World in a single event before subsequently spreading to the Afrotropical region. The ancestral hosts reconstructed for Myriophora are the benzoquinone‐producing Juliformia, and this association has been retained in the Old World clade. In the Neotropical region, Myriophora that are associated with cyanide‐producing polydesmidan millipedes are confined to a single clade that shows remarkably little genetic variation between clearly morphologically diagnosable species.     

Morphological convergence and molecular divergence: the taxonomic status of Sceloporus serrifer (squamata,phrynosomatidae) subspecies

Martínez‐Méndez, N., Mejía, O., Rocha‐Gómez, A. & Méndez‐De La Cruz, F. R. (2012) Morphological convergence and molecular divergence: the taxonomic status of Sceloporus serrifer (squamata, phrynosomatidae) subspecies. —Zoologica Scripta, 41, 97–108. The systematics of the subspecies included in Sceloporus serrifer has undergone several taxonomic and nomenclatural rearrangements. This species previously comprised two recognized subspecies, Sceloporus serrifer serrifer and Sceloporus serrifer prezygus, which inhabit contrasting habitats. In this study, we re‐evaluate the taxonomic status of both subspecies using molecular and morphological evidence. Sceloporus serrifer serrifer was recovered as a paraphyletic group, whereas S. s. prezygus was recovered as a polyphyletic group. The molecular results indicate the existence of two independent lineages that diverged at least 1.29 Myr, with the populations currently recognized as S. s. prezygus from the Cuchumatanes Mountains representing a secondary invasion of S. s. serrifer from the lowlands. The lack of meristic differences among the highland populations of different species suggests convergence in similar environments achieved by two different lineages.     

Molecular survey of morphological subspecies reveals new mitochondrial lineages in Podarcis muralis (Squamata: Lacertidae) from the Tuscan Archipelago (Italy)

Recent analyses of molecular markers have significantly revised the traditional taxonomy of Podarcis species (Squamata: Lacertidae), leading to critically reconsider the taxonomic value of several subspecies described only on morphological bases. In fact, lizards often exhibit high morphological plasticity both at the intra‐specific and the intra‐population level, especially on islands, where phenotypic divergences are mainly due to local adaptation, rather than to evolutionary differentiation. The Common wall lizard Podarcis muralis exhibits high morphological variability in biometry, pholidosis values and colour pattern. Molecular analyses have confirmed the key role played by the Italian Peninsula as a multi‐glacial refuge for P. muralis, pointing out the lack of congruence between mitochondrial lineages and the four peninsular subspecies currently recognized. Here, we analyse a portion of the protein‐encoding cytochrome b gene in the seven subspecies described for the Tuscan Archipelago (Italy), in order to test whether the mitochondrial haplotypes match the morphologically based taxonomy proposed for Common wall lizard. We also compare our haplotypes with all the others from the Italian Peninsula to investigate the presence of unique genetic lineages in insular populations. Our results do not agree completely with the subspecific division based on morphology. In particular, the phylogenetic analyses show that at least four subspecies are characterized by very similar haplotypes and fall into the same monophyletic clade, whereas the other three subspecies are closer to peninsular populations from central Italy. From these results, we conclude that at least some subspecies could be better regarded as simple eco‐phenotypes; in addition, we provide an explanation for the distinctiveness of exclusive lineages found in the archipelago, which constituted a refuge for this species during last glacial periods.     

Mismatch of morphological and molecular identifications in native and invasive subspecies of Codium fragile (Bryopsidophyceae,Chlorophyta)

Several subspecies are defined within Codium fragile, including the invasive C. fragile ssp. fragile, first reported in New Zealand in 1973. An endemic subspecies, C. fragile ssp. novae‐zelandiae, is also found throughout New Zealand. The two subspecies exhibit morphological and molecular variation, although these have never been evaluated together. We compared variation between subspecies at locations in Auckland, identifying subspecies using rps3‐rpl16 DNA sequence data, and assessing gross morphological differences, anatomical utricle characters and morphometrics. The taxonomic utility of the morphometric data sets was assessed by linear discriminant analysis. Utricle characters and measurements varied within individual thalli and between different preservation methods. The phenotypes of both subspecies were highly variable and influenced by environment. Accurate subspecies delimitation using morphological data was not possible; the discriminant analyses performed no better than chance for all combinations of the morphological data. Specimens from New Zealand, Canada, Australia and Ireland were sequenced using both the rps3‐rpl16 and tufA plastid markers. The tufA elongation factor was shown to be a good candidate for differentiating subspecies of C. fragile. This marker is twice the length of the rps3‐rpl16 spacer, shows greater variation between ssp. fragile and novae‐zelandiae, and is less prone to sequencing error. A simple restriction enzyme digest of the tufA amplicon can distinguish ssp. fragile and ssp. novae‐zelandiae. Our study expands the known range of the ssp. fragile in New Zealand, including the first record of this subspecies from the west coast of Auckland, and points to a need to re‐evaluate morphological and molecular criteria for subspecies currently defined within C. fragile.     

The Golden and Mariana albatrosses,new species of pierid butterflies,with a review of subgenus Appias (Catophaga) (Lepidoptera)

This paper presents an overview of the subgenus Appias (Catophaga) Hübner (Pieridae). A beautiful golden‐yellow member of the group, endemic to the Indonesian island of Sulawesi, Appias (Catophaga) aurosa Yata & Vane‐Wright sp.n. , is described as new. A small white species, Appias (Catophaga) mariana Yata & Chainey sp.n. , is described as new from the Marianas. Four other taxa, A. (C.) athama (Blanchard), A. (C.) galba (Wallace) stat.rev. , A. (C.) galene (Felder & Felder) and A. (C.) wardii (Moore), treated in most recent literature as subspecies, are recognized here as distinct, increasing the number of Catophaga species generally recognized from nine to 15. A brief review is given for each, with notes on their diagnosis, general distribution and known hostplants. An annotated synonymic checklist indicating subspecies, type localities and four new synonyms, and nine lectotype designations, one neotype designation and two type locality restrictions necessary to stabilize usage conclude the paper. Online Supporting Information provides an extensive discussion concerning the possible evolution of these butterflies with respect to polymorphism, speciation, coloration and hostplant relationships, a comprehensive list of type material for all available species group names belonging to the subgenus, and a complete bibliography for all citations in both the printed and online material.     

The reproductive ecology of two subspecies of the bitterling Rhodeus atremius (Cyprinidae, Acheilognathinae)

The reproductive ecology of two endangered subspecies of the bitterling Rhodeus atremius was investigated in two rivers in Okayama and Fukuoka Prefectures, Japan. Several other bitterling species, R. ocellatus, Tanakia limbata, T. lanceolata, Acheilognathus tabira and A. rhombeus, are also found in these rivers. Spawning of both R. atremius subspecies was recorded between late March and August 2007, peaking between April and July. Females of R. atremius began to mature at small body size (minimum 25 mm). They had small clutch sizes (maximum 16 eggs) and developed a short ovipositor (mean 13.6 mm), which was used to deposit a bulb-shaped egg of comparatively large size (3.2 mm³, major and minor axes 2.8 and 1.5 mm). Clutch size, ovipositor length and egg size appear to be a function of female body size. Both the body size and ovipositor length of R. atremius with ripe ova and the size and shape of the eggs varied seasonally. Rhodeus a. suigensis achieved maturity at a smaller body size, had a longer ovipositor and produced smaller eggs, with the minor axis being wider relative to the major axis than those of R. a. atremius. Rhodeus atremius may be adapted for depositing small numbers of eggs in a much shallower position inside the gills of smaller host mussels than other bitterling species.     

Fine‐scale patterns of genetic divergence within and between morphologically variable subspecies of the sea urchin Heliocidaris erythrogramma (Echinometridae)

The spatial scale over which genetic divergences occur between populations and the extent that they are paralleled by morphological differences can vary greatly among marine species. In the present study, we use a hierarchical spatial design to investigate genetic structure in Heliocidaris erythrogramma occurring on near shore limestone reefs in Western Australia. These reefs are inhabited by two distinct subspecies: the thick‐spined Heliocidaris erythrogramma armigera and the thin‐spined Heliocidaris erythrogramma erythrogramma, each of which also have distinct colour patterns. In addition to pronounced morphological variation, H. erythrogramma exhibits a relatively short (3–4 days) planktonic phase before settlement and metamorphosis, which limits their capacity for dispersal. We used microsatellite markers to determine whether patterns of genetic structure were influenced more by morphological or life history limitations to dispersal. Both individual and population‐level analyses found significant genetic differentiation between subspecies, which was independent of geographical distance. Genetic diversity was considerably lower within H. e. erythrogramma than within H. e. armigera and genetic divergence was four‐fold greater between subspecies than among populations within subspecies. This pattern was consistent even at fine spatial scales (< 5 km). We did detect some evidence of gene flow between the subspecies; however, it appears to be highly restricted. Within subspecies, genetic structure was more clearly driven by dispersal capacity, although weak patterns of isolation‐by‐distance suggest that there may be other factors limiting gene exchange between populations. Our results show that spatial patterns of genetic structure in Western Australian H. erythrogramma is influenced by a range of factors but is primarily correlated with the distribution of morphologically distinct subspecies. This suggests the presence of reproductive barriers to gene exchange between them and demonstrates that morphological variation can be a good predictor of genetic divergence. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 578–592.     

Intraspecific genetic variation in the common midwife toad (Alytes obstetricans): subspecies assignment using mitochondrial and microsatellite markers

The common midwife toad (Alytes obstetricans), widely distributed in the northern half of the Iberian Peninsula and part of Western Europe, is currently subdivided into four subspecies: A. o. obstetricans, A. o. boscai, A. o. pertinax and A. o. almogavarii. However, the delimitation of these subspecies and their ranges are still under discussion because strong discordances have been found between morphological and molecular data, and especially among different genetic markers. Here, we screen a set of novel microsatellite loci and mtDNA sequences of A. obstetricans populations representative of all currently recognized subspecies to investigate the correspondence between genetic groupings inferred from clustering analysis of microsatellite genotypes and the described subspecies and test whether patterns of mtDNA variation are concordant with those genetic clusters. Our results confirm previous expectations of extremely high intraspecific diversity in A. obstetricans in Iberia. Analyses of microsatellite and mtDNA data were concordant in recovering five well‐defined groups, of which three correspond to previously defined subspecies, while the two additional clusters correspond to populations of subspecies A. o. boscai separated by the Douro River. Our results suggest the occurrence of two distinct genetic units within A. o. boscai that likely result from a long independent evolutionary history, thus deserving special attention from a conservation point of view.     

Contrasting patterns of polymorphism and selection in bacterial‐sensing toll‐like receptor 4 in two house mouse subspecies

Detailed investigation of variation in genes involved in pathogen recognition is crucial for understanding co‐evolutionary processes between parasites and their hosts. Triggering immediate innate response to invading microbes, Toll‐like receptors (TLRs) belong presently among the best‐studied receptors of vertebrate immunity. TLRs exhibit remarkable interspecific variation and also intraspecific polymorphism is well documented. In humans and laboratory mice, several studies have recently shown that single amino acid substitution may significantly alter receptor function. Unfortunately, data concerning polymorphism in free‐living species are still surprisingly scarce. In this study, we analyzed the polymorphism of Toll‐like receptor 4 (Tlr4) over the Palearctic range of house mouse (Mus musculus). Our results reveal contrasting evolutionary patterns between the two recently (0.5 million years ago) diverged house mouse subspecies: M. m. domesticus (Mmd) and M. m. musculus (Mmm). Comparison with cytochrome b indicates strong directional selection in Mmd Tlr4. Throughout the whole Mmd western Palaearctic region, a single variant of the ligand‐binding region is spread, encoded mainly by one dominant haplotype (71% of Mmd). In contrast, Tlr4 in Mmm is much more polymorphic with several haplotypes at intermediate frequencies. Moreover, we also found clear signals of recombination between two principal haplogroups in Mmm, and we identified eight sites under positive selection in our dataset. Our results suggest that observed differences in Tlr4 diversity may be attributed to contrasting parasite‐mediated selection acting in the two subspecies.     

Mitochondrial phylogeography and subspecies of the wide‐ranging sub‐Saharan leopard tortoise Stigmochelys pardalis (Testudines: Testudinidae) – a case study for the pitfalls of pseudogenes and GenBank sequences

The leopard tortoise (Stigmochelys pardalis) is the most widely distributed sub‐Saharan tortoise species, with a range extending from the Horn of Africa all over eastern Africa to the Republic of South Africa, Namibia and southernmost Angola. Using 1938 bp of mitochondrial DNA (cyt b gene, partial ND4 gene plus adjacent tRNA genes) from a nearly range‐wide sampling, we examined its phylogeographic structure and compared our findings with previously published GenBank sequences. We identified seven major clades that are largely parapatrically distributed. A few records of distinct haplotypes at the same locality or in close proximity could be the result of translocation of tortoises by man. The greatest diversity occurs in the south of the species’ range, with five out of the seven clades. Testing for isolation‐by‐distance suggests that the observed phylogeographic structure is the result of restricted geographical gene flow and not of historical vicariance. This is in sharp contrast to wide‐ranging thermophilic reptiles from the western Palaearctic, whose phylogeographic structure was significantly shaped by Pleistocene range interruptions, but also by earlier dispersal and vicariant events. Most cyt b sequences of S. pardalis from GenBank turned out to be nuclear pseudogenes, or to be of chimerical origin from such pseudogenes and authentic mitochondrial sequences, which argues for caution regarding uncritical usage of GenBank sequences. The recent revalidation of the two subspecies of S. pardalis was based on such a chimerical sequence that was erroneously identified with the subspecies S. p. babcocki. Furthermore, according to our data, the distribution of mitochondrial clades does match neither the traditional subspecies ranges nor the pronounced geographical size variation of leopard tortoises. We conclude that there is no rationale for recognizing subspecies within S. pardalis.     

A revision of the Appalachian millipede genus Brachoria Chamberlin, 1939 (Polydesmida: Xystodesmidae: Apheloriini)

The apheloriine millipede genus Brachoria as presented here comprises 34 species distributed throughout the south‐eastern US Appalachian Mountains. Members of this genus are blind (like all millipedes in the order Polydesmida), large (4–6 cm in length), and display conspicuous aposematic coloration in yellow, red, orange, and violet. Many Brachoria species participate in Müllerian mimicry rings with co‐occurring Apheloriini, in particular with species in the genus Apheloria. Some areas contain five co‐mimic species of Apheloriini and a high local density totalling 43 individuals per 50 m². Since the first revision in 1959, workers have suggested that many more species were awaiting discovery in the Cumberland Mountains. Here I present a taxonomic revision and describe ten new species: Brachoria badbranchensis , Brachoria blackmountainensis , Brachoria campcreekensis , Brachoria cumberlandmountainensis , Brachoria flammipes , Brachoria grapevinensis , Brachoria guntermountainensis , Brachoria hendrixsoni , Brachoria sheari , and Brachoria virginia . Five of these new species occur in the Cumberland Mountain Thrust Block region and five occur elsewhere throughout the Appalachian Highlands in eastern Kentucky, north‐eastern Alabama, southern West Virginia, south‐western Virginia, and the Blue Ridge Mountains of Tennessee. A molecular phylogeny of Brachoria species is well supported at deeper divergences, corresponds closely with geography, and is used as a phylogenetic basis for the taxonomy presented here. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 159 , 817–889.     

Climate rather than geography separates two European honeybee subspecies

Both climatic and geographical factors play an important role for the biogeographical distribution of species. The Carpathian mountain ridge has been suggested as a natural geographical divide between the two honeybee subspecies Apis mellifera carnica and A. m. macedonica. We sampled one worker from one colony each at 138 traditional apiaries located across the Carpathians spanning from the Hungarian plains to the Danube delta. All samples were sequenced at the mitochondrial tRNA^Leu‐cox2 intergenic region and genotyped at twelve microsatellite loci. The Carpathians had only limited impact on the biogeography because both subspecies were abundant on either side of the mountain ridge. In contrast, subspecies differentiation strongly correlated with the various temperature zones in Romania. A. m. carnica is more abundant in regions with the mean average temperature below 9 °C, whereas A. m. macedonica honeybees are more frequent in regions with mean temperatures above 9 °C. This range selection may have impact on the future biogeography in the light of anticipated global climatic changes.     

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.     

Taxonomy and evolution of thesinica group of macaques: I. Species and subspecies accounts ofMacaca sinica

Based on study of 116 museum specimens and review of relevant literature, a new species account ofMacaca sinica, the Sri Lanka toque macaque, is presented. External and cranial characters of the species are described and analyzed. A summary of natural history of the species includes information on habitats, arboreal-terrestrial preferences, predators, diet, relations with other primate species, density, troop size and composition, home range area, and reproductive biology. Two subspecies ofM. sinica are recognized, northernM. s. sinica (Linnaeus, 1771) and southwesternM. s. aurifrons (Pocock, 1931). Geographic ranges of these two subspecies meet in a 50–200 km broad contact zone in which representatives of both subspecific phenotypes are encountered (35s. sinica phenotypes; 8s. aurifrons phenotypes in 43 contact zone specimens examined). An annotated gazetteer of known macaque localities in Sri Lanka provides information concerning available museum specimens and field reports by collectors or observers. Comparative study of three remaining species in thesinica group (M. radiata, M. assamensis, & M. thibetana) is in progress. This research was partly supported by National Institutes of Health MBS Grant No. RR-08043 to Chicago State University.     

Scope for genetic rescue of an endangered subspecies though re‐establishing natural gene flow with another subspecies

Genetic diversity is positively linked to the viability and evolutionary potential of species but is often compromised in threatened taxa. Genetic rescue by gene flow from a more diverse or differentiated source population of the same species can be an effective strategy for alleviating inbreeding depression and boosting evolutionary potential. The helmeted honeyeater Lichenostomus melanops cassidix is a critically endangered subspecies of the common yellow‐tufted honeyeater. Cassidix has declined to a single wild population of ~130 birds, despite being subject to intensive population management over recent decades. We assessed changes in microsatellite diversity in cassidix over the last four decades and used population viability analysis to explore whether genetic rescue through hybridization with the neighbouring Lichenostomus melanops gippslandicus subspecies constitutes a viable conservation strategy. The contemporary cassidix population is characterized by low genetic diversity and effective population size (N_e < 50), suggesting it is vulnerable to inbreeding depression and will have limited capacity to evolve to changing environments. We find that gene flow from gippslandicus to cassidix has declined substantially relative to pre‐1990 levels and argue that natural levels of gene flow between the two subspecies should be restored. Allowing gene flow (~4 migrants per generation) from gippslandicus into cassidix (i.e. genetic rescue), in combination with continued annual release of captive‐bred cassidix (i.e. demographic rescue), should lead to positive demographic and genetic outcomes. Although we consider the risk of outbreeding depression to be low, we recommend that genetic rescue be managed within the context of the captive breeding programme, with monitoring of outcomes.     

Reflectance of sexually dichromatic UV‐blue patches varies during the breeding season and between two subspecies of Gallotia galloti (Squamata: Lacertidae)

Body coloration is sexually dimorphic in many vertebrate species, including lizards, in which males are often more conspicuous than females. A detailed analysis of the relative size of coloured patches and their reflectance, including the ultraviolet (UV) range, has rarely been performed. In the present work we quantified sexual dimorphism in body traits and surface area of all lateral patches from adult females and males of two subspecies of Gallotia galloti (G. g. galloti and G. g. eisentrauti). We also analysed the magnitude of sexual dichromatism in the UV‐visible reflectance of such patches and the changes in patch size and brightness during the reproductive season (April–July). Males had significantly larger patch areas (relative to their snout‐vent length) and higher brightness (mainly in the UV‐blue range) than did females in both subspecies. The comparison of relative patch areas among months did not reach statistical significance. However, patch brightness significantly changed during the breeding season: that of the UV‐blue (300–495 nm) range from lizards of the two subspecies was significantly larger in June than in April, while brightness in the 495–700 nm range in G. g. galloti was larger in May, June, and July than in April. A different pattern of dichromatism was also detected in the two populations, with G. g. eisentrauti being more sexually dichromatic than G. g. galloti. We discuss the results in terms of possible evolutionary causes for the sexual dichromatism related to different ecological characteristics of the habitats where each subspecies live. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 556–569.