Phylogenetic analysis of cryptic speciation in the polychaete Pygospio elegans

Development in marine invertebrate species can take place through a variety of modes and larval forms, but within a species, developmental mode is typically uniform. Poecilogony refers to the presence of more than one mode of development within a single species. True poecilogony is rare, however, and in some cases, apparent poecilogony is actually the result of variation in development mode among recently diverged cryptic species. We used a phylogenetic approach to examine whether poecilogony in the marine polychaete worm, Pygospio elegans, is the result of cryptic speciation. Populations of worms identified as P. elegansooded, and intermediate larvae; these modes are found both within and among populations. We examined sequence variation among partial mitochondrial cytochrome c oxidase subunit I sequences obtained for 279 individual worms sampled across broad geographic and environmental scales. Despite a large number of unique haplotypes (121 haplotypes from 279 individuals), sequence divergence among European samples was low (1.7%) with most of the sequence variation observed within populations, relative to the variation among regions. More importantly, we observed common haplotypes that were widespread among the populations we sampled, and the two most common haplotypes were shared between populations differing in developmental mode. Thus, our results support an earlier conclusion of poecilogony in P elegans. In addition, predominantly planktonic populations had a larger number of population-specific low-frequency haplotypes. This finding is largely consistent with interspecies comparisons showing high diversity for species with planktonic developmental modes in contrast to low diversity in species with brooded developmental modes.     

Out of Africa: the slow train to australasia

We used mitochondrial DNA (mtDNA) sequences to test biogeographic hypotheses for Patiriella exigua (Asterinidae), one of the world's most widespread coastal sea stars. This small intertidal species has an entirely benthic life history and yet occurs in southern temperate waters of the Atlantic, Indian, and Pacific oceans. Despite its abundance around southern Africa, southeastern Australia, and several oceanic islands, P. exigua is absent from the shores of Western Australia, New Zealand, and South America. Phylogenetic analysis of mtDNA sequences (cytochrome oxidase I, control region) indicates that South Africa houses an assemblage of P. exigua that is not monophyletic (P = 0.04), whereas Australian and Lord Howe Island specimens form an interior monophyletic group. The placement of the root in Africa and small genetic divergences between eastern African and Australian haplotypes strongly suggest Pleistocene dispersal eastward across the Indian Ocean. Dispersal was probably achieved by rafting on wood or macroalgae, which was facilitated by the West Wind Drift. Genetic data also support Pleistocene colonization of oceanic islands (Lord Howe Island, Amsterdam Island, St. Helena). Although many biogeographers have speculated about the role of long-distance rafting, this study is one of the first to provide convincing evidence. The marked phylogeographic structure evident across small geographic scales in Australia and South Africa indicates that gene flow among populations may be generally insufficient to prevent the local evolution of monophyly. We suggest that P. exigua may rely on passive mechanisms of dispersal.     

Intraspecific Variation in the Vocalizations and Hand Pad Morphology of Southern Lesser Bush Babies (Galago moholi): A Comparison with G. senegalensis

Previous studies have shown the taxonomic value of vocal repertoires and hand (volar) pad characteristics in the classification of cryptic nocturnal primates such as bush babies. However, no study included quantitative comparisons within the geographical range of any one species. We investigated levels of intraspecific variation in calls and hand pad characteristics of the southern lesser bush baby (Galago moholi), using the northern lesser bush baby (Galago senegalensis) for interspecific comparisons. Examination of calls recorded from different regions along a transect of 1500 km across southern Africa revealed low levels of intraspecific variation in Galago moholi, whereas comparisons with homologous call-types in G. senegalensis revealed them to be significantly different. Volar pad measurements across the ranges of both species also showed low levels of intraspecific variation and relatively high interspecific variation. These findings demonstrate that vocal and volar pad characteristics can be used as consistent measures of difference between species that look almost identical. These methods provide a practical means of distinguishing between cryptic species, whether in the field, in captivity, or, in the case of volar pads, of preserved specimens.     

Allelic inheritance in naturally occurring parthenogenetic offspring of the gonochoric sea star Patiria miniata

Abstract. In laboratory studies of fertilization using the gonochoric broadcast-spawning asterinid sea star Patiria miniata , we found many cases in which some mature eggs spawned by females formed cleavage-stage embryos and feeding bipinnaria larvae without fertilization by sperm. Segregation of maternal microsatellite alleles among the parthenogenetic offspring of known heterozygous females was consistent with several specific modes of asexual reproduction, including polar body suppression. Cryptic outcrossing by sperm contamination was ruled out by the failure to observe non-maternal alleles. The potential for asexual reproduction by the normally outcrossing members of P. miniata may suggest a shared propensity for asexuality among asterinid species from several clades in which isolated adults can produce offspring without outcrossing.     

Reproduction and larval morphology of broadcasting and viviparous species in the Cryptasterina species complex

The Cryptasterina group of asterinid sea stars in Australasia comprises cryptic species with derived life histories. C. pentagona and C. hystera have planktonic and intragonadal larvae, respectively. C. pentagona has the gonochoric, free-spawning mode of reproduction with a planktonic lecithotrophic brachiolaria larva. C. hystera is hermaphroditic with an intragonadal lecithotrophic brachiolaria, and the juveniles emerge through the gonopore. Both species have large lipid-rich buoyant eggs and well-developed brachiolariae. Early juveniles are sustained by maternal nutrients for several weeks while the digestive tract develops. C. hystera was reared in vitro through metamorphosis. Its brachiolariae exhibited the benthic exploration and settlement behavior typical of planktonic larvae, and they attached to the substratum with their brachiolar complex. These behaviors are unlikely to be used in the intragonadal environment. The presence of a buoyant egg and functional brachiolaria larva would not be expected in an intragonadal brooder and indicate the potential for life-history reversal to a planktonic existence. Life-history traits of species in the Cryptasterina group are compared with those of other asterinids in the genus Patiriella with viviparous development. Modifications of life-history traits and pathways associated with evolution of viviparity in the Asterinidae are assessed, and the presence of convergent adaptations and clade-specific features associated with this unusual mode of parental care are examined.     

Evidence of hidden biodiversity, ongoing speciation and diverse patterns of genetic structure in giant Antarctic amphipods

Recent molecular research on Antarctic benthic organisms has challenged traditional taxonomic classifications, suggesting that our current perceptions of Antarctic biodiversity and species distributions must be thoroughly revised. Furthermore, genetic differentiation at the intraspecific level remains poorly understood, particularly in eastern Antarctica. We addressed these issues using DNA sequence data for two sibling amphipod species that could be collected on a circum-Antarctic scale: Eusirus perdentatus and Eusirus giganteus. Haplotype networks and Bayesian phylogenies based on mitochondrial (COI, CytB) and nuclear (ITS2) DNA provided strong evidence of multiple cryptic species of Eusirus, with several occurring in sympatry and at least one likely to have a true circum-Antarctic distribution. Within species, gene flow was often highly restricted, consistent with a brooding life history and in some cases suggestive of current or future allopatric speciation. Patterns of genetic structure were not always predictable: one cryptic species showed preliminary evidence of high genetic differentiation across ～150 km in eastern Antarctica (F(ST) > 0.47, P < 0.01), yet another was remarkably homogenous across ～5000 km (F(ST) = 0.00, P = 1.00). Genetic diversity also varied among cryptic species, independent of sample size (π = 0.00-0.99). These results indicate several hidden levels of genetic complexity in these Antarctic amphipods that are neither apparent from previous taxonomic or ecological studies nor predictable from their life history. Such genetic diversity and structure may reflect different modes of survival for Antarctic benthic organisms during historic glacial cycles, and/or subsequent re-establishment of populations on the shelf, and highlight our misunderstanding of Antarctic marine species diversity.     

Species-level diversification of African dwarf crocodiles (Genus Osteolaemus): A geographic and phylogenetic perspective

The taxonomy of the African dwarf crocodile (genus Osteolaemus) has been disputed since a novel morphotype was discovered in the early 20th Century. Because this poorly-known reptile is widely hunted throughout the forests of Central and West Africa, resolving the existence and extent of taxonomic units has important management and conservation implications. Lack of molecular data from individuals of known origin and historical disagreement on diagnostic morphological characters have hindered attempts to settle one of the most important taxonomic questions in the Crocodylia. In an effort to clarify the evolutionary relationships among dwarf crocodiles, we sequenced three mitochondrial and two nuclear genes using a large sample of dwarf crocodiles from known localities across major drainage basins of forested Africa. Concordant results from Bayesian, maximum likelihood, maximum parsimony and population aggregation analytical methods support a previously recognized division of the dwarf crocodile into a Congo Basin form (O. osborni) and a West African form (Osteolaemus tetraspis), but also reveal a third diagnosable lineage from West Africa warranting recognition as an separate taxonomic unit. Corrected genetic distances between geographic regions ranged from 0.2% to 0.6% in nuclear fragments and 10.0 to 16.2% in mitochondrial COI. Population aggregation, using fixed and alternate character (nucleotide) states to cluster or divide populations, recovered 232 such molecular characters in 4286 bp of sequence data and unambiguously aggregated populations into their respective geographic clade. Several previously recognized morphological differences coincide with our molecular analysis to distinguish Congo Basin crocodiles from the Ogooué Basin and West Africa. Discrete morphological characters have not yet been documented between the latter two regions, suggesting further work is needed or molecular data may be required to recognize taxonomic divisions in cases where putative species are morphologically cryptic. This study highlights the importance of using widespread taxon sampling and a multiple evidence approach to diagnose species boundaries and reveal cryptic diversity.     

Systematics of the olive thrush Turdus olivaceus species complex with reference to the taxonomic status of the endangered Taita thrush T. helleri

During the last 40 years, few species of African birds have undergone more taxonomic revision than the olive thrush Turdus olivaceus. This is due to disagreement on how to partition the striking phenotypic variation among allopatric populations. The current consensus is to recognise one species T. olivaceus , split into three assemblages: (1) the olivaceus group restricted to southern Africa, (2) the swynnertoni group of the Zimbabwean and southern Malawi highlands, and (3) the abyssinicus group of the montane highlands of eastern and central Africa. Mitochondrial DNA sequences from 63 individuals were analysed to investigate the phylogenetic relationships among 16 taxa (species and subspecies) in the olivaceus species complex (plus seven outgroup species), with, particular emphasis on the relationships and taxonomic status of the endangered Taita thrush ( helleri ). Phylogenetic hypotheses generated using parsimony, maximum likelihood, and Bayesian inference identified a number of discrete clades corresponding to recognised subspecies. Northern ( abyssinicus clade) and southern populations ( olivaceus + swynnertoni clade) of olive thrush differ by 9–10% in sequence divergence. Furthermore, all analytical methods suggested that helleri (Taita Hills) and roehli (Usambara and Pare Mountains) are reciprocally monophyletic with respect to mtDNA, and 2.5 to 10.5% divergent from all other forms of olive thrush. Both helleri and roehli are surrounded in adjacent highlands by populations of olive thrush that represent a more recent radiation, suggesting that helleri and roehli may be relict taxa which have been able to maintain their genetic integrity. The results of this study support previous arguments for recognizing the arid/woodland T. smithi as a species distinct from other southern African forest populations of T. olivaceus (including the swynnertoni group). Results further suggest that T. abyssinicus , T. helleri , and T. roehli be accorded species rank.     

Life history diversity and evolution in the Asterinidae

Asterinid sea stars have the greatest range of life historiesknown for the Asteroidea. Larval form in these sea stars hasbeen modified in association with selection for planktonic,benthic, or intergonadal developmental habitats. Life historydata are available for 31 species and molecular data for 28of these. These data were used to assess life history evolutionand relationships among asterinid clades. Lecithotrophy is prevalentin Asterinidae, with at least 6 independent origins of thisdevelopmental mode. Morphological differences in the attachmentcomplex of brachiolaria larvae were evident among species withplanktonic lecithotrophy. Some features are clade specific whileothers are variable within clades. Benthic brachiolariae aresimilar in Aquilonastra and Parvulastra with tripod-shaped larvae,while the bilobed sole-shaped larvae of Asterina species appearunique to this genus. Multiple transitions and pathways havebeen involved in the evolution of lecithotropy in the Asterinidae.Although several genera have a species with a planktonic feedinglarva in a basal phylogenetic position, relative to specieswith planktonic or benthic lecithotrophy, there is little evidencefor the expected life history transformation series from planktonicfeeding, to planktonic non-feeding, to benthic non-feeding development.Intragonadal development, a life history pattern unique to theAsterinidae, arose three times through ancestors with benthicor pelagic lecithotrophy. Evolution of lecithotrophy appearsmore prevalent in the Asterinidae than other asteroid families.As diverse modes of development are discerned in cryptic speciescomplexes, new insights into life history evolution in the Asterinidaeare being generated.     

How many conservation units are there for the endangered grassland earless dragons?

Species are the most commonly recognised unit for conservation management, yet significant variation can exist below the level of taxonomic recognition and there is a lack of consensus around how a species might be defined. This definition has particular relevance when species designations are used to apportion conservation effort and when definitions might be made through legislation. Here, we use microsatellite DNA analyses to test the proposition that the last remaining populations of the endangered grassland earless dragon (Tympanocryptis pinguicolla) harbour substantial cryptic genetic variation. Our study provides strong evidence that long historical isolation and the recent impacts of urbanization, have led to genetic differentiation in microsatellite DNA allele frequencies and high numbers of private alleles among three genetic clusters. This differentiation is partially concordant with previous mitochondrial DNA analyses, which show the two regions (Canberra and Monaro) where this species exists, to be reciprocally monophyletic, but differs through the identification of a third genetic cluster that splits a northern Canberra cluster from that of southern Canberra. Our data also identify a stark contrast in population genetic structure between clusters such that high levels of genetic structure are evident in the highly urbanised Canberra region but not in the largely rural Monaro region. We conclude that this species, like many reptiles, harbours considerable cryptic variation and currently comprises three distinct and discrete units. These units could be classified as separate species for the purpose of conservation under the relevant Australian and international Acts drawing management appropriate to that status.     

The cushion–star Parvulastra exigua in South Africa: one species or more?

The cushion–star Parvulastra exigua (Lamarck, 1816) is a widely distributed member of the temperate intertidal fauna in the southern hemisphere. In South Africa, it occurs in sympatry with the endemic Parvulastra dyscrita (Clark, 1923), the two species being differentiated predominantly by gonopore placement. Several recent studies have suggested that there may be additional cryptic species within the Parvulastra exigua complex in South Africa, based variously on color morphology, genetic evidence and the differential placement of the gonopores. This paper attempts to resolve whether one or more species are represented within Parvulastra exigua. A total of 346 Parvulastra exigua and 8 Parvulastra dyscrita were collected from sites on the west and south–west coasts of South Africa; morphological, anatomical and genetic analyses were performed to determine whether cryptic species and/or Parvulastra exigua specimens with aboral gonopores were present. Results show that neither cryptic species nor Parvulastra exigua specimens with aboral gonopores occur at these sites. This study thus refutes previous claims of the existence of aboral gonopores in South African Parvulastra exigua, and suggests that a single species is represented. The distinction between Parvulastra exigua and Parvulastra dyscrita is also confirmed, and features separating these two species are clarified and documented.     

Molecular identification of some forensically important blowflies of southern Africa and Australia

One major aspect of research in forensic entomology is the investigation of molecular techniques for the accurate identification of insects. Studies to date have addressed the corpse fauna of many geographical regions, but generally neglected the southern African calliphorid species. In this study, forensically significant calliphorids from South Africa, Swaziland, Botswana and Zimbabwe and Australia were sequenced over an 1167 base pair region of the COI gene. Phylogenetic analysis was performed to examine the ability of the region to resolve species identities and taxonomic relationships between species. Analyses by neighbour-joining, maximum parsimony and maximum likelihood methods all showed the potential of this region to provide the necessary species-level identifications for application to post-mortem interval (PMI) estimation; however, higher level taxonomic relationships did vary according to method of analysis. Intraspecific variation was also considered in relation to determining suitable maximum levels of variation to be expected during analysis. Individuals of some species in the study represented populations from both South Africa and the east coast of Australia, yet maximum intraspecific variation over this gene region was calculated at 0.8%, with minimum interspecific variation at 3%, indicating distinct ranges of variation to be expected at intra- and interspecific levels. This region therefore appears to provide southern African forensic entomologists with a new technique for providing accurate identification for application to estimation of PMI.     

Geographic Variation of Photoperiodic Diapause but Not Adult Survival or Reproduction of the Invasive Mosquito Aedes albopictus (Diptera: Culicidae) in North America

Climate differences across latitude can result in seasonal constraints and selection on life-history characters. Because Aedes albopictus (Skuse) invaded North America in the mid-1980s, it has spread across a range of ≈14° latitude and populations in the north experience complete adult mortality because of cold winter temperatures that are absent in the south. Life-table experiments were conducted to test for differences in the adult survival and reproductive schedules of Ae. albopictus females from three populations from the northern (Salem, NJ; Springfield, IL; Eureka, MO; ≈39° N) and southern (Palm Beach, Palmetto, Tampa, FL; ≈27-28° N) extremes of the species distribution in North America. There were consistent differences between northern and southern populations in incidence of photoperiodically-induced egg diapause. Under short daylength, diapause eggs constituted twice the proportion of total viable eggs from northern females (81.9-92.1%) than southern females (35.9-42.7%). There were no consistent differences between northern and southern populations in resource allocation between reproduction and maintenance, reproduction over time, and reproductive investment among offspring, and no apparent trade-offs between diapause incidence with reproduction or longevity. Our results suggest that the main response of North American Ae. albopictus to unfavorable winter climates is via the life history strategy of producing diapausing eggs, rather than quantitative variation in reproduction, and that there are no detectable costs to adult survival. Inherent geographic variation in the expression of diapause, consistent with the latitudinal extremes of A. albopictus, indicates evolutionary loss of diapause response in southern populations because of the invasion of A. albopictus in North America.     

Intraspecific variation of cuticular hydrocarbon profiles in the Anastrepha fraterculus (Diptera: Tephritidae) species complex

The goal of this study was to define whether cuticular hydrocarbons (CHs) could be used for taxonomic determination of putative species hidden in the Anastrepha fraterculus cryptic species complex, widespread from Argentina to Mexico. Recently, increasing evidence of phenotypic and genetic variability has resulted in the characterization of eight morphotypes within this complex. The CH profiles of six A. fraterculus populations from Argentina, Brazil, Peru, Colombia and Mexico were analysed in this study by two‐dimensional gas chromatography coupled with mass spectrometry. In parallel, multiple factorial analyses were used to elucidate population structures. Vector populations segregated into four distinct groups. The analysis demonstrated that the studied populations from Peru, Argentina and southern Brazil (Vacaria) might be classified in accordance with the earlier division of the A. fraterculus complex into Peruvian, and Brazilian‐1 cryptic species, using the specific CH profiles. Population from south‐eastern Brazil (Piracicaba) formed separated group. Mexican and Andean (Colombian) putative species had similar CH signatures, when compared to each other.     

Test of colonisation scenarios reveals complex invasion history of the red tomato spider mite Tetranychus evansi

The spider mite Tetranychus evansi is an emerging pest of solanaceous crops worldwide. Like many other emerging pests, its small size, confusing taxonomy, complex history of associations with humans, and propensity to start new populations from small inocula, make the study of its invasion biology difficult. Here, we use recent developments in Approximate Bayesian Computation (ABC) and variation in multi-locus genetic markers to reconstruct the complex historical demography of this cryptic invasive pest. By distinguishing among multiple pathways and timing of introductions, we find evidence for the "bridgehead effect", in which one invasion serves as source for subsequent invasions. Tetranychus evansi populations in Europe and Africa resulted from at least three independent introductions from South America and involved mites from two distinct sources in Brazil, corresponding to highly divergent mitochondrial DNA lineages. Mites from southwest Brazil (BR-SW) colonized the African continent, and from there Europe through two pathways in a "bridgehead" type pattern. One pathway resulted in a widespread invasion, not only to Europe, but also to other regions in Africa, southern Europe and eastern Asia. The second pathway involved the mixture with a second introduction from BR-SW leading to an admixed population in southern Spain. Admixture was also detected between invasive populations in Portugal. A third introduction from the Brazilian Atlantic region resulted in only a limited invasion in Europe. This study illustrates that ABC methods can provide insights into, and distinguish among, complex invasion scenarios. These processes are critical not only in understanding the biology of invasions, but also in refining management strategies for invasive species. For example, while reported observations of the mite and outbreaks in the invaded areas were largely consistent with estimates of geographical expansion from the ABC approach, historical observations failed to recognize the complex pathways involved and the corresponding effects on genetic diversity.     

Two in one: cryptic species discovered in biological control agent populations using molecular data and crossbreeding experiments

There are many examples of cryptic species that have been identified through DNA‐barcoding or other genetic techniques. There are, however, very few confirmations of cryptic species being reproductively isolated. This study presents one of the few cases of cryptic species that has been confirmed to be reproductively isolated and therefore true species according to the biological species concept. The cryptic species are of special interest because they were discovered within biological control agent populations. Two geographically isolated populations of Eccritotarsus catarinensis (Carvalho) [Hemiptera: Miridae], a biological control agent for the invasive aquatic macrophyte, water hyacinth, Eichhornia crassipes (Mart.) Solms [Pontederiaceae], in South Africa, were sampled from the native range of the species in South America. Morphological characteristics indicated that both populations were the same species according to the current taxonomy, but subsequent DNA analysis and breeding experiments revealed that the two populations are reproductively isolated. Crossbreeding experiments resulted in very few hybrid offspring when individuals were forced to interbreed with individuals of the other population, and no hybrid offspring were recorded when a choice of mate from either population was offered. The data indicate that the two populations are cryptic species that are reproductively incompatible. Subtle but reliable diagnostic characteristics were then identified to distinguish between the two species which would have been considered intraspecific variation without the data from the genetics and interbreeding experiments. These findings suggest that all consignments of biological control agents from allopatric populations should be screened for cryptic species using genetic techniques and that the importation of multiple consignments of the same species for biological control should be conducted with caution.     

The invasion history of the exotic freshwater zooplankter Daphnia lumholtzi (Cladocera, Crustacea) in North America: a genetic analysis

Daphnia lumholtzi is a planktonic crustacean native to subtropical regions in Africa, Asia and Australia. Since its invasion to the southern USA in ~1990 it has spread across North America as far north as the Laurentian Great Lakes. We assessed invasion history using microsatellite makers and to explore the influence of mean annual temperature on the genetic structure along a latitudinal gradient in North America. Genotypic data were obtained from 9 microsatellite markers for 178 individuals from 13 populations (eight populations introduced to North America and five populations in the native range). Pairwise F_st values as well as Bayesian clustering showed a strong subdivision between native and introduced populations. Bayesian clustering identified multiple genetic clusters in recently invaded locations, suggestive of multiple invasions from various sources, including Asia and Africa. Using variation partitioning, we determined the amount of variation for genetic clusters of populations in the invaded range due to mean annual air temperature and the year of first detection. The results point to a primary introduction into the southern range of North America, with a subsequent northward expansion, and multiple introductions possibly from both the native range and by secondary spread from previously-invaded locations. Separate analysis of genetic clusters within the invaded range suggests additional effects of temperature conditions on geographic genetic structure, possibly as a consequence of D. lumholtzi’s tropical origin.     

SEX RATIO VARIATION IN THE LESSONIA NIGRESCENS COMPLEX (LAMINARIALES,PHAEOPHYCEAE): EFFECT OF LATITUDE,TEMPERATURE, AND MARGINALITY1

Little is known about variation of sex ratio, the proportion of males to females, in natural populations of seaweed, though it is a major determinant of the mating system. The observation of sexual chromosomes in kelps suggested that sex is partly genetically determined. However, it is probably not purely genetic since the sex ratio can be modified by environmental factors such as salinity or temperature. In this paper, sex ratio variation was studied in the kelp Lessonia nigrescens Bory complex, recently identified as two cryptic species occurring along the Chilean coast: one located north and the other south of the biogeographic boundary at latitude 29°–30° S. The life cycle of L. nigrescens is characterized by an alternation of microscopic haploid gametophytic individuals and large macroscopic fronds of diploid sporophytes. The sex ratio was recorded in progenies from 241 sporophytic individuals collected from 13 populations distributed along the Chilean coast in order (i) to examine the effect of an environmental gradient coupled with latitude, and (ii) to compare marginal populations to central populations of the two species. In addition, we tested the hypothesis that the sex ratios of the two cryptic species would be affected differently by temperature. First, our results demonstrate that sex ratio seems to be mainly genetically determined and temperature can significantly modify it. Populations of the northern species showed a lower frequency of males at 14°C than at 10°C, whereas populations of the southern species showed the opposite pattern. Second, both species displayed an increased variation in sex ratio at the range limits. This greater variation at the margins could be due either to differential mortality between sexes or to geographic parthenogenesis (asexual reproduction).