Do taxonomic divisions reflect genetic differentiation? A comparison of morphological and genetic data in Coenonympha tullia (Müller), Satyrinae

Historically, morphological variation has been used to classify many species (and subspecies) of Lepidoptera. However, some of this variation may be unsuitable for inferring the recent evolutionary history of populations. Genetic data provide an alternative. We examine the morphological and genetic variation within and between British subspecies of Coenonympha tullia (Müller 1764) to test the hypothesis that neutral genetic variation corresponds to morphological variation. We find that most morphological and genetic variation occurs within populations and that those populations designated as subspecies based on morphological characters are not necessarily most closely related for mitochondrial DNA or nuclear DNA (amplified fragment length polymorphisms and allozymes). Thus, the notion that wing spot variation reflects population isolation and therefore genetic differentiation does not hold. The present study highlights the need for genetic data where taxonomy may be based on environmentally plastic or locally adapted characters because such characters will not reflect the true population genetic history.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 314–327.     

Intraspecific taxonomy and ecology characterize morphological divergence among cutthroat trout (Oncorhynchus clarkii ssp. Richardson) populations

We compared the proportion of morphological variation accounted for by subspecies categories with the proportion encompassed by ecologically based categories in cutthroat trout ( Oncorhynchus clarkii ssp.), as a means of assessing the relative importance of each approach in identifying intraspecific diversity. We used linear and geometric morphometrics to compare measures of body shape, fin length, and head features between and within subspecies of cutthroat trout. Both categories accounted for a significant proportion of the variation between and within the subspecies; however, the larger proportion was explained by subspecific differences, with the greatest morphological divergence between coastal cutthroat trout ( Oncorhynchus clarkii clarkii ) and interior subspecies. Ecotypic categories within each subspecies also explained significant morphological differences: stream populations had longer fins and deeper, more robust bodies than lake populations. The largest ecotypic differences occurred between stream and lake populations of Yellowstone cutthroat trout ( Oncorhynchus clarkii bouvieri ). Given that many cutthroat trout subspecies are of conservation concern, our study offers a better understanding of intraspecific variation existing within the species, providing precautionary evidence of incipient speciation, and a framework of describing phenotypic diversity that is correlated with ecological conditions.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 266–281.     

Phylogeny and species boundaries in the gobiid genus Gnatholepis (Teleostei: Perciformes)

Species of the goby genus Gnatholepis Bleeker, 1874, are common inhabitants of shallow tropical seas worldwide. In this study, mitochondrial DNA sequence (ND2 gene), from 349 Gnatholepis individuals sampled from across the South and Central Pacific and Caribbean, is used to infer phylogeny and determine species boundaries. Seven species of Gnatholepis are recognized: the Indo-Pacific G. anjerensis (Bleeker, 1851) [ G. cauerensis (Bleeker, 1853) is a synonym]; G. scapulostigma Herre, 1953; G. davaoensis Seale, 1910; G. knighti Jordan & Evermann, 1903; G. gymnocara Randall & Greenfield, 2001; G.  sp. Randall & Greenfield, 2001; and the Atlantic/Caribbean G. thompsoni Jordan, 1904. Results from the molecular phylogeny are compared with a previous morphology-based revision of the genus in order to establish which morphological characters diagnose species in correspondence with the molecular phylogeny.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 142 , 573–582.     

An integrative approach to species delimitation in Benthomangelia (Mollusca: Conoidea)

DNA sequences are currently used to propose primary hypotheses of species delimitation, especially when morphological variability is difficult to assess. In an integrative taxonomy framework, these hypotheses are then compared with other characters, such as morphology or geography, to produce robust species delimitations. For this purpose, the cytochrome oxidase subunit I (COI) gene has been sequenced for almost 50 specimens of the genus Benthomangelia , a deep-sea marine gastropod genus, collected in the South-West Pacific. Five genetic groups, displaying low and high genetic distances respectively within and between groups, were defined. COI hypotheses were compared with both the results obtained with the independent nuclear 28S gene and with an elliptic Fourier analysis of the shape of the last whorl of the shell. 28S gene analysis confirmed the same well-supported groups as COI, and elliptic Fourier analysis identified several morphological characters that vary similarly to genetic variability.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 696–708.     

Systematics and evolutionary relationships of the mountain lizard Liolaemus monticola (Liolaemini): how morphological and molecular evidence contributes to reveal hidden species diversity

The delimitation of species is a major issue in systematic biology and has been a re-emerging discipline in the last decade. A number of studies have shown that the use of multiple data sets is critical for the identification of cryptic species, particularly in groups with complex evolutionary histories. Liolaemus monticola is a montane lizard species distributed in central Chile (32°–42°S), with four described subspecies in a latitudinal gradient from north to south: L. m. monticola , L. m. chillanensis , L. monticola ssp. and L. m. villaricensis . In order to test the systematic status and phylogenetic relationships of the taxa included in the L. monticola group, we analysed morphological (morphometric and meristic) and molecular (allozyme and mitochondrial DNA) data sets. The results of the morphological analyses showed that meristic variables correctly assigned individuals with higher accuracy than did morphometric characters. The results of the analyses of allozyme data revealed eight diagnostic loci that are evidence for significant differences among the four L. monticola subspecies. Phylogenetic analyses with mitochondrial DNA data, including additional species, showed that the L. monticola group is polyphyletic. We postulate that the four current subspecies represent independent evolutionary lineages and must be raised to the specific level as L. monticola , L. chillanensis and L. villaricensis . The taxonomic status of the unnamed L. monticola ssp. remains unresolved, although we provide a preliminary proposal.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 635–650.     

New distributional and molecular information call into question the systematic position of the West Asian Viola sintenisii (Violaceae)

The west Asian Viola sintenisii W.Becker, described from temperate woodlands of northern Iran and south-western Turkmenistan on the Caspian coast, was long considered a vicariant geographical subspecies of the mainly south European V. alba Besser. The new findings of V. sintenisii in four geographically separated stations in north-eastern Azerbaijan significantly expands its range of distribution. These occurrences are within the range of V. alba ssp. alba . Here the two taxa frequently co-occur but remain distinct and V. sintenisii is therefore justified at species level. It is likely that the two species are also sympatric in the Hyrcanian region, a range previously attributed uniquely to the latter. Viola sintenisii seems to be fairly common in the eastern parts of the Great Caucasus, but there are reasons to suggest that it has there been misinterpreted as V. suavis . The chromosome number of V. sintenisii , 2 n  = 20, is reported here for the first time.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 147 , 91–98.     

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.     

The diversity and biogeography of koa-finches (Drepanidini: Rhodacanthis), with descriptions of two new species

All known populations of koa-finches, genus Rhodacanthis , became extinct in the Holocene epoch. Two new species are described here from Quaternary fossil sites in the Hawaiian Islands. One new species, from Kauai and Maui, is roughly the size of the historically known greater koa-finch ( R. palmeri ) but differs in having a more robust skull and in bill morphology. The second new species, from Oahu and Maui, is similar in size to the lesser koa-finch ( R. flaviceps ) but closer to R. palmeri in qualitative osteological traits. The two species of koa-finches known historically from the island of Hawaii are distinct in osteology from the fossil koa-finches on the older Hawaiian islands, indicating that at least two of the four known speciation events in the genus took place within approximately the past 500 kyr. However, the similarity of maxillae from Pleistocene and Holocene sites on Oahu suggests that the Oahu population maintained morphological stasis through the climate changes of the late Quaternary. The evidence that speciation occurred on the youngest island in the archipelago suggests that the process of community assembly on newly emergent Hawaiian landscapes was a stimulus to evolutionary diversification in Rhodacanthis .  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 527–541.     

Minuartia graminifolia (Caryophyllaceae), a south-east European species

A re-evaluation of Minuartia graminifolia has been undertaken based on comparative morphological studies. M. graminifolia subsp. rosani (an endemic of the south-central Apennines and Sicily) and subsp. hungarica (an endemic of the Banat region of Romania) are accepted infraspecific taxa. M. graminifolia subsp. hungarica is lectotypified. M. graminifolia subsp. clandestina is confirmed for Italy; the taxon is neotypified. The type subspecies is considered an endemic to the east-central Alps. Keys to the species of Minuartia ser. Graminifoliae and to the subspecies of M. graminifolia are provided.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 143 , 419–432.     

Iris stenophylla Hausskn. & Siehe ex Baker from Turkey and its cytology

A morphological study, both in the field and from herbarium material, showed that there are no convincing characteristics separating the Turkish endemics Iris stenophylla ssp. stenophylla and ssp. allisonii . A cytological survey revealed chromosome numbers of 2 n  = 24, 26 and 26 + 1B. No variation in either chromosome number or karyotype was found in ssp. allisonii , which always had 2 n  = 26, although the chromosome number and karyotypes of ssp. stenophylla were variable. Since neither morphological nor cytological differences were sufficient to separate the two subspecies, I. stenophylla ssp. allisonii is therefore reduced to a synonym of I. stenophylla .  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 115−127.     

Taxonomic relevance of the gametophytic generation in a strictly rupicolous fern group: Asplenium seelosii s.l.

The systematics of the Asplenium seelosii complex has been debated for a long time. This complex includes strictly rupicolous plants that live on limestone cliffs mainly in the mountains of south-west Europe: the Alps, the Pyrenees, and several mountain ranges of the eastern Iberian Peninsula. The disjunct distribution of its populations and several morphological characters, i.e. leaf indumentum and the structure of the perispore, have been used to distinguish two species and up to four subspecies. The goal of this study was to determine whether the characters of the gametophytic generation and young sporophytes can contribute to the recognition of the proposed taxa. The analysis of all of these characters together differentiated two groups that correspond to the established species, A. seelosii and A. celtibericum , but not enough differences were found to separate the subspecies in each of them.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 375–386.     

Conflicting patterns of genetic and morphological variation in European Gentianella section Gentianella

Genetics in European Gentianella Moench sect. Gentianella were investigated using internal transcribed spacer (ITS) nrDNA, trn L-F cpDNA and Amplified Fragment Length Polymorphisms (AFLP) fingerprint data to analyse relationships within the section. Both a cladistic and a phenetic approach, as well as nonhierarchical analysis (PCA) and partitioning of molecular variance (AMOVA), were used. Sequence data did not resolve groups within the section. They reflected, however, geographical isolation between central European and eastern Carpathian ( G. lutescens and G. bulgarica ) as well as Caucasian samples ( G. caucasea ). AFLP data revealed a strong differentiation within G. germanica between populations of the Alps and north-western middle Europe, although there is hardly any morphological differentiation of taxonomic significance. Morphological similarities between G. aspera and G. pilosa were not reflected in genetics, and no support was found for G. aspera . Genetic similarities were not in line with morphology in G. lutescens and G. bulgarica . AFLP data only partly resolve relationships among taxa. High genetic similarities, as well as partitioning of molecular variance among taxa/populations of eastern middle Europe ( G. austriaca , G. bohemica , G. germanica , G. stiriaca ) and intermediate morphological characters in G. bohemica and G. stiriaca , might indicate reticulate evolution. The overall low sequence divergence within the section points to a very young origin of all taxa.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 175–187.     

Taxonomic relationships of the western Asian taxa of Gentiana sect. Pneumonanthe

The taxonomic position of western Asian members of Gentiana sect. Pneumonanthe has long been a matter of conflict. In this paper, the six western Asian species currently recognized as belonging to sect. Pneumonanthe ( G. boissieri , G. calycina , G. freyniana , G. gelida , G. paradoxa , and G. septemfida ) are compared and their relationships established using a morphological phylogenetic analysis. Seed testa and flower and leaf morphological characters were studied and 11 characters were selected for a cladistic analysis. Euro-Siberian and Far Eastern taxa of sect. Pneumonanthe ( G. pneumonanthe and G. scabra ) were used as outgroups. Our results suggest the presence of two morphologically distinct clades within the western Asian gentians: a Septemfida and a Gelida clade. G. calycina and G. freyniana show close affinities to G. boissieri and G. gelida , and are distinct from G. septemfida s.l. Biogeographical aspects of the two groups are discussed.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 152 , 197–208.     

Genetic differentiation and gene flow of two sparidae subspecies, Diplodus sargus sargus and Diplodus sargus cadenati in Atlantic and south-west Mediterranean populations

A total of nine enzymes coded by 14 loci were assayed for each of six populations (from the north-eastern Atlantic and the Mediterranean) of two sea bream subspecies ( Diplodus sargus sargus and Diplodus sargus cadenati ). Diagnostic alleles were observed for each subspecies, although there were several common alleles. Estimates of variance in allele frequencies among samples ( F _ST) revealed significant differences ( P  < 0.05) among both subspecies. Genetic divergence was found between Atlantic and Mediterranean samples: values for genetic distances were higher than 0.163. Furthermore, D. sargus cadenati populations displayed a higher mean weight and length than D. sargus sargus populations and significant differences in growth were found among subspecies and populations. These results are discussed in terms of levels of gene flow and its respective relationships with water circulation in the Strait of Gibraltar and geological events.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 705–717.     

Complex patterns of morphological and mtDNA variation in Lacerta perspicillata (Reptilia; Lacertidae)

Lacerta perspicillata is a north-west African lacertid lizard that shows considerable intraspecific variation, with three subspecies described on the basis of colour pattern and body size. Recent observations of a population containing two morphological forms and more than one deep genetic lineage, as well as an apparent lack of concordance between forms and genetic lineages, suggest that the complexity is greater than previously thought. To analyse and quantify this variation, we studied the variability within this species at two levels: (1) external morphology (multivariate analysis of scalation, body dimensions, and colour pattern) and (2) mtDNA (sequencing and single-strand confirmation polymorphism analysis). Fifty-two individuals were studied at Taza, northern Morocco. Two morphological groupings (ostensibly representing two previously described subspecies) and two deep mtDNA lineages were detected at this site, with complete correspondence between the two. This, together with an apparent lack of hybrids, would normally support respective full species recognition. However, analysis of 98 individuals from other populations demonstrated that the situation is highly complex with the same genetic lineages having reversed morphotypes in other areas, making such a designation difficult. Across the other studied populations, we found no support for any of the currently recognized subspecies. The lack of congruence between mtDNA lineages and morphometric patterns (in some cases) and the morphological similarity among lizards from different lineages suggest ecophenotypic convergence or multiple introgressive hybridization. The study highlights the tremendous complexity that may exist within a taxon and the inadequacy of older alpha-taxonomy based designations in describing it.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 479–490.     

Phylogeography and subspecies taxonomy of dunlins (Calidris alpina) in western Palearctic analysed by DNA microsatellites and amplified fragment length polymorphism markers

In a circumpolar wader, the dunlin ( Calidris alpina ), there are 11 named subspecies, but only five mitochondrial DNA (mtDNA) lineages have been found. In the present study, we investigated the genetic structure of dunlins in western Palearctic (from East Greenland to Taimyr peninsula) using DNA microsatellites and amplified fragment length polymorphism (AFLP) markers that may detect more recent differentiation than mtDNA. In this region, we consider four described subspecies; alpina , schinzii , arctica and centralis , together comprising two mtDNA lineages. We analyse seven polymorphic microsatellite loci and 91 AFLP markers in 287 and 152 unrelated individuals, respectively, originating from 17 populations. Neither microsatellites nor AFLPs reveal distinct groups that correspond to currently recognized subspecies. There is a clear pattern of isolation by distance in microsatellites. Our results do not contradict the former mtDNA results that there are two phylogenetic lineages (approximately corresponding to schinzii and centralis ) that have met and formed a cline ( alpina ). We find no difference between schinzii and arctica (East Greenland). We conclude that, given the lack of distinct groups and the gradual changes in microsatellite allele frequencies, these markers provide little genetic support for the dunlin subspecies taxonomy in the western Palearctic.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 713–726.     

Sophora sect. Edwardsia (Fabaceae): further evidence from nrDNA sequence data of a recent and rapid radiation around the Southern Oceans

Phylogenetic relationships are inferred from nuclear ribosomal internal transcribed spacer sequences for species belonging to Sophora sect. Edwardsia from South America, New Zealand, Lord Howe Island, Hawai'i, La Réunion, Easter Island, and Raivavae Island (French Polynesia). Results support the monophyly of sect. Edwardsia , but relationships among the species from this section are poorly resolved due to most species having identical sequences. The origin of Sophora sect. Edwardsia is discussed, as competing hypotheses have proposed the group originated in South America from a North American ancestor, or in the north-west Pacific. We suggest sect. Edwardsia may have arisen in the north-west Pacific from a Eurasian ancestor.  © The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 435–441.     

Genetic and morphological divergence reveals local subdivision of perch (Perca fluviatilis L.)

The level of gene flow is an important factor influencing genetic differentiation between populations. Typically, geographic distance is considered to be the major factor limiting dispersal and should thus only influence the degree of genetic divergence at larger spatial scales. However, recent studies have revealed the possibility for small-scale genetic differentiation, suggesting that the spatial scale considered is pivotal for finding patterns of isolation by distance. To address this question, genetic and morphological differentiation were studied at two spatial scales (range 2–13 km and range 300 m to 2 km) in the perch ( Perca fluviatilis L.) from the east coast archipelago of Sweden, using seven microsatellite loci and geometric morphometrics. We found highly significant genetic differentiation between sampled locations at both scales. At the larger spatial scale, the distance per se was not affecting the level of divergence. At the small scale, however, we found subtle patterns of isolation by distance. In addition, we also found morphological divergence between locations, congruent with a spatial separation at a microgeographic scale, most likely due to phenotypic plasticity. The present study highlights the importance of geographical scale and indicates that there might be a disparity between the dispersal capacity of a species and the actual movement of genes. Thus, how we view the environment and possible barriers to dispersal might have great implications for our ability to fully understand the evolution of genetic differentiation, local adaptation, and, in the end, speciation.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 746–758.     

Amplified fragment length polymorphism genetic fingerprinting challenges the taxonomic status of the near-endemic species Chara curta Nolte ex Kütz. (Characeae)

Amplified fragment length polymorphism (AFLP) genetic fingerprinting of 14 accessions of Chara curta and Chara aspera Willd., sampled across a range of habitats and morphologies in Britain, suggests that these taxa are part of the variation within a single species complex. Two primer combinations generating 397 fragments (97% of which were polymorphic), analysed by Jaccard's similarity coefficient and principal co-ordinate analysis, did not recover groups which reflect the current taxonomy. By contrast with the genetic study, a Gower general similarity coefficient and principal co-ordinate analysis of 52 morphological characters recovered the currently recognized species groups. A Mantel test showed no significant correlation between the genetic data and the morphological data, supporting the hypothesis that phenotypic variability in Chara L. is either to some extent environmentally induced or represents developmental stages. Implications for the conservation status of C. curta in Britain are discussed.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 467–476.