Population analysis using the nuclear white gene detects Pliocene/Pleistocene lineage divergence within Anopheles nuneztovari in South America

Anopheles (Nyssorhynchus) nuneztovari Gabaldón (Diptera: Culicidae), a locally important malaria vector in some regions of South America, has been hypothesized to consist of at least two cryptic incipient species. We investigated its phylogeographic structure in several South American localities to determine the number of lineages and levels of divergence using the nuclear white gene, a marker that detected two recently diverged genotypes in the primary Neotropical malaria vector Anopheles darlingi Root. In An. nuneztovari, five distinct lineages (1-5) were elucidated: (1) populations from northeastern and central Amazonia; (2) populations from Venezuela east and west of the Andes; (3) populations from Colombia and Venezuela west of the Andes; (4) southeastern and western Amazonian Brazil populations, and (5) southeastern and western Amazonian Brazil and Bolivian populations. There was a large amount of genetic differentiation among these lineages. The deepest and earliest divergence was found between lineage 3 and lineages 1, 2 and 4, which probably accounts for the detection of lineage 3 in some earlier studies. The multiple lineages within Amazonia are partially congruent with previous mtDNA and ITS2 data, but were undetected in many earlier studies, probably because of their recent (Pleistocene) divergence and the differential mutation rates of the markers. The estimates for the five lineages, interpreted as recently evolved or incipient species, date to the Pleistocene and Pliocene. We hypothesize that the diversification in An. nuneztovari is the result of an interaction between the Miocene/Pliocene marine incursion and Pleistocene climatic changes leading to refugial isolation. The identification of cryptic lineages in An. nuneztovari could have a significant impact on local vector control measures.     

Historical diversification of floodplain forest specialist species in the Amazon: a case study with two species of the avian genus Xiphorhynchus (Aves: Dendrocolaptidae)

Phylogeographical and population genetics methods are used to reconstruct the diversification history of two species of the genus Xiphorhynchus (Aves: Dendrocolaptidae) associated with seasonally flooded forest types in Amazonia. Sequences of the mitochondrial gene cytochrome b were assessed for 21 and 30 individuals, belonging to eight and ten populations, of Xiphorhynchus kienerii and Xiphorhynchus obsoletus , respectively. Uncorrected genetic distances among unique haplotypes recovered ranged only from 0.01% to 0.4% for both species. Over 90% of the genetic variation detected in both species was partitioned within populations, and therefore was not structured geographically. Mismatch distributions and values of Tajima's D -tests indicate that both X. kienerii and X. obsoletus have had small evolutionary effective population sizes, but experienced a recent demographic expansion. These demographic expansions are tentatively dated as occurring over the last 18 000 years BP, a time frame which coincides with the establishment of the early and mid-Holocene age floodplain forest in most of central and eastern Amazonia, following a period of increased river stages throughout the basin. Based on phylogenetic, phylogeographical, and populations genetics data obtained for X. kienerii and X. obsoletus , an evolutionary scenario is proposed to account for the historical diversification of floodplain specialist species in Amazonia.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 383–395.     

Local adaptation in a plant herbivore interaction depends on the spatial scale

Local adaptation has central importance in the understanding of co-evolution, maintenance of sexual reproduction, and speciation. We investigated local adaptation in the alkaloid-bearing legume Crotalaria pallida and its seed predator, the arctiid moth Utetheisa ornatrix , at different spatial scales. When we studied three populations from south-east Brazil (150 km apart), we did not find evidence of local adaptation, although we did find interpopulational differences in herbivore performance, and a significant interaction between herbivore sex and plant population. These results indicate that both moth and plant populations are differentiated at the regional scale. In a comparison of populations from Brazil and Florida, the herbivore showed local adaptation to its host plant; for both moth populations, the pupae were heavier when the larvae ate the sympatric than the allopatric host population. We discuss the scale dependence of our results and the possible causes for the lack of local adaptation at the regional scale, even in the presence of plant and moth differentiation. The results obtained demonstrate the importance of studying co-evolution and local adaptation at different geographical scales.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 494–502.     

Population structure in the catfish Trichogenes longipinnis: drift offset by asymmetrical migration in a tiny geographic range

Based on population genetic theory and empirical studies of small populations, we expect that species with very small ranges (narrow endemics) will exhibit reduced genetic diversity, increasing their susceptibility to the negative effects of genetic homogeneity. Although this pattern of reduced diversity applies to most narrow endemics, conservation biologists have yet to identify a general pattern for the degree of spatial population genetic structure expected in species with very small ranges. In part, this is because the degree of population structure within narrow endemics will be highly variable depending on the equilibrium between the homogenizing effects of dispersal and the diversifying effects of drift and local selection in small populations, thus precluding general predictions about the relative importance of small range, small population sizes, and habitat patchiness for maintaining genetic diversity in narrowly-distributed species. We document a striking example of high population structure in the tiny geographic range of a stream-dwelling catfish, Trichogenes longipinnis , endemic to the Atlantic Forest of Brazil. The maintenance of this diversity results from a combination of asymmetrical and limited dispersal, and drift in small populations. Our results highlight the need to understand population structure, and not only overall genetic diversity, of narrowly-distributed species for their conservation planning.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 259–274.     

Delturinae, a new loricariid catfish subfamily (Teleostei, Siluriformes), with revisions of Delturus and Hemipsilichthys

A new subfamily, Delturinae, is described to accommodate the loricariid catfish genera Delturus Egenmann & Eigenmann, 1889 and Hemipsilichthys Eigenmann & Eigenmann, 1889, a clade recently demonstrated to be the sister group of all remaining loricariids except Lithogenes . The genus Hemipsilichthys is restricted to three species, H. gobio (Lütken, 1874), its sister species H. papillatus Pereira et al ., 2000, and H. nimius Pereira et al ., 2003. Relationships among species of Delturus were not resolved and a new species, D. brevis , is described from the Rio Jequitinhonha basin in eastern Brazil. The geographical distribution of Delturinae, exclusively on the south-eastern Brazilian Shield, indicates that south-eastern Brazil acts as either a refugium for basal loricariid taxa or a point of origin for the Loricariidae. Lectotypes are designated for D. parahybae Eigenmann & Eigenmann, 1889 and Plecostomus angulicauda Steindachner, 1877. Keys are presented for subfamilies of Loricariidae and for genera and species of Delturinae. Diagnoses are provided for all delturine clades and species.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 147 , 277–299.     

A new species of Betula section Betulaster (Betulaceae) from China

A new species of Betulaceae, Betula fujianensis , is described and illustrated from Luoboyan Reserve, Fujian Province, south-eastern China. Betula fujianensis is distributed in subtropical evergreen and deciduous broad-leaved mixed forest at elevations above 500 m, mostly as scattered individuals and occasionally as populations alone or with B. luminifera . Betula fujianensis belongs to section Betulaster and differs from other species in general morphology and phenology. A key to all species currently recognized in this section is presented, and the relationships between the new species and its closely related taxa are discussed.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 156 , 523–528.     

Pindamoraria boraceiae, a new genus and species of freshwater Canthocamptidae (Copepoda, Harpacticoida) from Brazil

Members of a new genus and species of harpacticoid copepod crustacean appeared in samples from semi-terrestrial (moist arboreal mosses, wet soil) and aquatic (bromeliad tanks, Sphagnum moss, rock pools, stream) habitats in a remnant of the Atlantic Forest in south-eastern Brazil. The new taxon, for which we propose the name Pindamoraria boraceiae sp. nov. , is distinguished by a unique combination of characters, in particular the segmentation and setation pattern of legs 1–4 in both sexes, the structure of leg 5 in the female, and the strongly modified claw of the maxilliped in the male. It most resembles the canthocamptid genera Moraria , Pseudomoraria , Morariopsis and Paramorariopsis . Both previous records of species of Moraria from South America refer to members of Antarctobiotus , which is not considered a member of the Moraria group: Moraria (Kuehneltiella) neotropica Löffler has previously been transferred to Antarctobiotus ; and we propose herein the transfer of Moraria kummeroworum Ebert & Noodt to Antarctobiotus as well. In the New World, the genus Moraria extends only as far south as Honduras; and Pseudomoraria , Morariopsis and Paramorariopsis are Old World genera. The new species from Brazil is therefore the only member of the Moraria group known from South America.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 139, 81–92.     

Genetic discontinuities among populations of Cleistes (Orchidaceae, Vanilloideae) in North America

Genetic patterns were examined in five populations of North American Cleistes with three sources of molecular data: amplified fragment length polymorphisms (AFLP), DNA sequencing, and plastid microsatellites. Populations of C. bifaria were sampled in four areas of the south-eastern US: the coastal plains of Florida and North Carolina and the mountains of North Carolina and West Virginia. A population of C. divaricata sympatric with the North Carolina coastal plain C. bifaria was also sampled. Analysis of the three types of molecular data resulted in the same relationships among the five sampled populations. The coastal plain population of C. divaricata was consistently grouped with the C. bifaria populations from the mountains of West Virginia and North Carolina, and the two coastal plain populations of C. bifaria formed a separate group, results not supporting the existing concepts of species relationships. For future studies, greater sampling of C. divaricata populations and more detailed morphological and phenological studies are recommended for better characterization of the diversity within North American Cleistes . © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 145 , 87–95.     

Chromosome numbers in wild and semidomesticated Brazilian Capsicum L. (Solanaceae) species: do x = 12 and x = 13 represent two evolutionary lines?

Chromosome numbers were determined in 29 accessions of wild and semidomesticated Capsicum species from the EMBRAPA Hortaliças (Brazil) germplasm collection. 2 n  = 24 was found in C. baccatum var. praetermissum , C. chinense , C. flexuosum and C. parvifolium , while C. buforum , C. campylopodium , C. cornutum , C. schottianum , C. villosum var. villosum and five other native south-eastern Brazilian species not yet taxonomically named all had 2 n  = 26 chromosomes. These are the first chromosome number determinations for C. cornutum , C. schottianum , C. villosum var. villosum and the five other Brazilian taxa. Our data confirm published data for C. baccatum var. praetermissum , C. campylopodium , C. chinense , C. flexuosum and C. parvifolium , but not for C. buforum . The prevalence of 2 n  = 26 chromosomes among Brazilian species, along with the morphological and ecological characteristics presented by the wild and semidomesticated species occurring in Brazil, form a pattern different from that found in Andean wild and semidomesticated species. This supports the hypothesis that there are two different evolutionary lines in the genus and that the native south-eastern Brazilian species belong to the ancestral Capsicum gene pool. © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 259–269.     

Genetic variation and structure in native populations of the fire ant Solenopsis invicta: evolutionary and demographic implications

We studied population genetic variation and structure in the fire ant Solenopsis invicta using nuclear genotypic and mitochondrial DNA (mtDNA) sequence data obtained from samples collected throughout its native range. Geographic populations are strongly differentiated at both genomes, with such structure more pronounced in Brazil than in Argentina. Higher-level regional structure is evident from the occurrence of isolation-by-distance patterns among populations, the recognition of clusters of genetically similar, geographically adjacent populations by ordination analysis, and the detection of an mtDNA discontinuity between Argentina and Brazil coinciding with a previously identified landform of biogeographical relevance. Multiple lines of evidence from both genomes suggest that the ancestors of the ants we studied resembled extant northern Argentine S. invicta , and that existing Brazilian populations were established more recently by serial long-distance colonizations and/or range expansions. The most compelling evidence for this is the corresponding increase in F _K (a measure of divergence from a hypothetical ancestor) and decrease in genetic diversity with distance from the Corrientes population in northern Argentina. Relatively deep sequence divergence among several mtDNA clades, coupled with geographical partitioning of many of them, suggests prolonged occupation of South America by S. invicta in more-or-less isolated regional populations. Such populations appear, in some cases, to have come into secondary contact without regaining the capacity to freely interbreed. We conclude that nominal S. invicta in its native range comprises multiple entities that are sufficiently genetically isolated and diverged to have embarked on independent evolutionary paths.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 541–560.     

Investigating South American biogeographic history using patterns of skull shape variation on Cerdocyon thous (Mammalia: Canidae)

Patterns of geographic variation of the canid Cerdocyon thous have historically been obscured by its remarkable intraspecific morphological variability. The observed distribution is highly associated with phytophysiognomy, a feature considered highly dynamic along geological time. In the present study, we tested whether vegetation distribution during the Holocene Glacial Maximum of South America (HGM) explains the patterns of morphological variation within Cerdocyon thous . The species was divided in groups according to paleohabitats that could support their presence during the HGM, and then tested for differences in skull morphometrics. The results obtained demonstrate that the climatic changes during the HGM influenced the population structure of this species, resulting in the establishment of geographical groups with different degrees of morphological cohesion. Higher morphological cohesion found in the Northern group might be explained by the marked discontinuity between its geographical range and the rest of the species'distribution. The Eastern and Southern morphological divergence is less striking and, although this could be related to past vegetation distribution, the disappearance of those barriers leads to a population structure that could be slowly breaking down.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 77–84.     

Three fishes in one: cryptic species in an Amazonian floodplain forest specialist

Accurately describing biodiversity in tropical regions such as Amazonia is difficult because of insufficient morphological inventories and the lack of studies on the distribution of genetic diversity. Aquatic organisms from Amazonian flooded forests are generally expected to move laterally along the forests during the annual inundation cycle, a behaviour that should promote admixture of populations and reduce within‐drainage speciation. We used an unprecedented fine‐scale sampling effort and multiple DNA markers to quantify region‐wide population differentiation in an Amazonian floodplain forest specialist, the black‐wing hatchet fish Carnegiella marthae ( Myers, 1927 ). Our study revealed three previously unsuspected and ancient cryptic species of black‐wing hatchet fish in the Rio Negro floodplain (RNF), in central Amazonia. Two species produce occasional first‐generation hybrids. The third and rarer species, although found in extreme sympatry with another species, appears to be reproductively isolated, and also differs in external morphology and dentition. Our findings have important implications for guiding conservation management because C. marthae is harvested commercially in the RNF ornamental fishery. They also suggest that the diversity of Amazonian ichthyofauna is vastly underestimated, including that found in landscapes lacking contemporary barriers to account for population divergence and speciation. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 391–403.     

Spatio-temporal genetic variation in sympatric and allopatric Mediterranean Cicada species (Hemiptera, Cicadidae)

Cicada barbara (Stål) and Cicada orni L. are two Mediterranean cicadas, very similar in morphology, that produce distinct acoustic mating signals and that have partially overlapping distribution ranges in the Iberian Peninsula, occurring in sympatry in several locations. In the present study, six microsatellite loci were analysed in C. barbara , four of which were also analysed in C. orni . Geographical and temporal genetic variation in these species was studied. No evidence of hybridization was found, enabling us to infer that the isolating barriers between these species are efficient. Partitioning of geographic variation in each species, revealed the following patterns: Iberian Peninsula and Northwestern African populations of C. barbara showed higher differentiation between than within each region, supporting C. barbara subspecific taxonomy ( C. barbara lusitanica in the Iberian Peninsula and C. barbara barbara in Northwestern Africa) and highlighting isolation coincident with the presence of physical barriers to gene-flow; differentiation between populations of C. orni from both sides of the Pyrenees was very low, and this mountain range may not constitute a significant barrier for the dispersal of this species; Greek populations of C. orni were found to be highly differentiated from Western European populations; and no pattern of isolation-by-distance was found in either species within the Iberian Peninsula.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 249–265.     

Life history evolution in a globally invading tephritid: patterns of survival and reproduction in medflies from six world regions

Comparisons among populations from different localities represent an important tool in the study of evolution. Medflies have colonized many temperate and tropical areas all over the world during the last few centuries. In a common garden environment, we examined whether medfly populations obtained from six global regions [Africa (Kenya), Pacific (Hawaii), Central America (Guatemala), South America (Brazil), Extra-Mediterranean (Portugal) and Mediterranean (Greece)] have evolved different survival and reproductive schedules. Whereas females were either short-lived [life expectancy at eclosion (e₀) 48–58 days; Kenya, Hawaii and Guatemala] or long-lived (e₀ 72–76 days; Greece, Portugal and Brazil], males with one exception (Guatemala) were generally long-lived (e₀ 106–122 days). Although males universally outlived females in all populations, the longevity gender gap was highly variable (20–58 days). Lifetime fecundity rates were similar among populations. However, large differences were observed in their age-specific reproductive patterns. Short-lived populations mature at earlier ages and allocate more of their resources to reproduction early in life compared with long-lived ones. In all populations, females experienced a post-reproductive lifespan, with this segment being significantly longer in Kenyan flies. Therefore, it seems plausible that medfly populations, inhabiting ecologically diverse habitats, have evolved different life history strategies to cope with local environmental conditions.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 106–117.     

Population divergence in the amphicarpic species Amphicarpaea edgeworthii Benth. (Fabaceae): microsatellite markers and leaf morphology

Comparative analyses of the genetic differentiation in microsatellite markers ( F _ST) and leaf morphology characters ( Q _ST) of Amphicarpaea edgeworthii Benth. were conducted to gain insight into the roles of random processes and natural selection in the population divergence. Simple sequence repeat analyses on 498 individuals of 19 natural populations demonstrate that a significant genetic differentiation occurs among populations (mean F _ST = 0.578), and A. edgeworthii is a highly self-fertilized species (mean selfing rate s  = 0.989). The distribution pattern of genetic diversity in this species shows that central populations possess high genetic diversity (e.g. population WL with H _E = 0.673 and population JG with H _E = 0.663), whereas peripheral ones have a low H _E as in population JD (0.011). The morphological divergence of leaf shape was estimated by the elliptical Fourier analysis on the data from 11 natural and four common garden populations. Leaf morphology analyses indicate the morphological divergence does not show strong correlation with the genetic differentiation ( R  = 0.260, P  = 0.069). By comparing the 95% confidence interval of Q _ST with that of F _ST, Q _ST values for five out of 12 quantitative traits are significantly higher than the average F _ST value over eight microsatellite loci. The comparison of F _ST and Q _ST suggests that two kinds of traits can be driven by different evolutionary forces, and the population divergence in leaf morphology is shaped by local selections.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 505–516.     

Fluvial range expansion, allopatry, and parallel evolution in a Danubian snail lineage (Neritidae: Theodoxus)

The snails Theodoxus danubialis and Theodoxus prevostianus form a single clade native to freshwaters of south-eastern Europe whose inter- and intraspecific relationships remain unresolved. The present study utilized a phylogeographical approach to clarify the relationship of these species as well as to reconstruct the evolutionary and demographic history of populations in the western portion of their range. Phylogenetic, population genetic, and nested clade analyses reveal a clade that has distributed itself upriver from a lower Danube River source population and become genetically distinct primarily through range expansion and localized allopatric divergence. Notably, this geographical pattern is replicated phylogenetically in the form of two cytochrome c oxidase subunit I (CO I) lineages that are present simultaneously in individual snails. Haplotypes from polymorphic individuals form two distinct clades, both of which show phylogenetic and nucleotide substitution patterns consistent with a mitochondrial origin, and whose common ancestor must have occurred in a lower Danube source population. Separated allopatrically from their Danubian relatives, populations of T. danubialis in northern Italy have also undergone substantial range expansion, much more recently than Danube watershed lineages. In addition to repeated patterns of range expansion, parallelism is found in T. prevostianus , which is shown to be a nonmonophyletic taxon of remarkable morphological and ecological similarity.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 603–617.     

Extremely low levels of genetic diversity in the terrestrial orchid Epipactis thunbergii (Orchidaceae) in South Korea: implications for conservation

Levels of allozyme variation, population genetic structure, and fine-scale genetic structure (FSGS) of the rare, both sexually and clonally reproducing terrestrial orchid Epipactis thunbergii were examined for eight ( N  = 734) populations in a 20 × 20-km area in South Korea. Twenty-three putative allozyme loci resolved from 15 enzyme systems were used. Extremely low levels of allozyme variation were found within populations: the mean frequency of polymorphic loci was 3.8% [isocitrate dehydrogenase ( Idh-2 ) with two alleles was polymorphic across populations], the mean number of alleles per locus was 1.04, and the mean expected heterozygosity was 0.013. The overall fixation index was not significantly different from zero ( F _IS = 0.069), although the species is self-compatible. However, a significantly high degree of population differentiation was found between populations at Idh-2 ( F _ST = 0.388) in the studied area. Furthermore, spatial autocorrelation analyses revealed a significant FSGS (up to 3 m) within populations. These observations suggest that the main explanatory factors for the extremely low levels of genetic diversity and the shaping of the population genetic structure of E. thunbergii are genetic drift as a result of a small effective population size, a restricted gene flow, and the isolation of populations. Considering the current genetic structure of E. thunbergii , three guidelines are suggested for the development of conservation strategies for the species in South Korea: (1) protection of habitats of standing populations; (2) prohibition by law of any collection of E. thunbergii ; and (3) protection of nearby pollinator populations, given the fact that fruit set in natural habitats is very low.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 161–169.     

Molecular characterization of an ancient Hepatozoon species parasitizing the 'living fossil' marsupial 'Monito del Monte' Dromiciops gliroides from Chile

The Microbiotheriid Dromiciops gliroides , also known as 'Monito del Monte', is considered to be a threatened species and the only living representative of this group of South American marsupials. During the last few years, several blood samples from specimens of 'Monito del Monte' captured at Chiloé island in Chile have been investigated for blood parasites. Inspection of blood smears detected a Hepatozoon species infecting red blood cells. The sequences of DNA fragments corresponding to small subunit ribosomal RNA gene revealed two parasitic lineages belonging to Hepatozoon genus. These parasite lineages showed a basal position with respect to Hepatozoon species infecting rodents, reptiles, and amphibians but are phylogenetically distinct from Hepatozoon species infecting the order Carnivora. In addition, the Hepatozoon lineages infecting D. gliroides are also different from those infecting other micro-mammals living in sympatry, as well as from some that have been described to infect an Australian species of bandicoot. The potential vector of this parasite appears to be the host-specific tick Ixodes neuquenensis because the sequencing of a long amplicon determined the presence of one of the two lineages found in the marsupial.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 568–576.     

Population genetic structure of New Zealand's endemic corophiid amphipods: evidence for allopatric speciation

Allozyme electrophoresis was used to examine population genetic structure at inter- and intraspecific levels for the New Zealand endemic corophiid amphipods, Paracorophium lucasi and P. excavatum. Individuals were collected from estuarine and freshwater habitats from North, South and Chatham Islands. Analyses of genetic structure among interspecific populations indicated clear allelic differentiation between the two Paracorophium species (Nei's genetic distance, D  = 1.62), as well as considerable intraspecific substructuring ( D  = 0.15–0.65). These levels of divergence are similar to interspecific levels for other amphipods and it is proposed that at least two groups from the P. lucasi complex and three from the P. excavatum complex correspond to sibling species. In most cases allopatry can account for the differentiation among the putative sibling species. For populations that share a common coastline we found low levels of differentiation and little or no correlation with geographical distance, suggesting that gene flow is adequate to maintain homogeneous population genetic structure. By contrast, populations on separate coastlines (i.e. isolated by land) showed moderate levels of geographical differentiation indicating restricted gene flow. The juxtaposition of population genetic and biogeographical data for Paracorophium in conjunction with the geological record infers past histories of glacial extirpation, and possible isolating effects of sea-level and landmass changes that have occurred throughout the Plio-Pleistocene.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 119–133.