Genetic diversity and differentiation in natural and reintroduced populations of Bencomia exstipulata and comparisons with B. caudata (Rosaceae) in the Canary Islands: an analysis using microsatellites

Variation at five polymorphic microsatellite loci was used to investigate genetic diversity and differentiation of two tetraploid Canarian endemics, Bencomia exstipulata and B. caudata. Data were analysed and are discussed in terms of tetrasomic (autotetraploid) and disomic (allotetraploid) inheritance. In both cases, genetic diversity values were similar to those described in other tetraploid plant species. High genetic differentiation between the only two described natural populations of B. exstipulata was detected (F_ST = 0.411). Bayesian cluster analysis revealed a geographical structure with distinct genetic groups from each island. High genetic differentiation and low genetic diversity of the B. exstipulata population from Tenerife suggest a recent population bottleneck, perhaps caused by the most recent major volcanic eruption, for this natural locality. This may be heightened by possible inbreeding depression and the monoecy of these species. Polymorphic microsatellite loci were also tested across all species in the Bencomia alliance. These reliably amplified the target sequence, suggesting a high degree of conservation of the sequences flanking the microsatellites. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 160 , 429–441.     

Genetic structure of the rare and endangered Hieracium wiesbaurianum group (Asteraceae) in Bavaria

The rare and endangered Hieracium wiesbaurianum species group shows a scattered relictual distribution in Bavaria. Recently, a couple of populations were discovered which clearly differ from all other populations. If these must be considered as taxonomically independent units, they would be of crucial conservation interest, because of the sole responsibility that Bavaria has for these worldwide endemics. We therefore analysed the genetic structure of H. wiesbaurianum in a comparative approach. Our analysis comprised 37 populations of 13 taxa of H. wiesbaurianum, H. bifidum and H. laevigatum, including three potentially new taxa. We applied amplified fragment length polymorphism (AFLP) analysis and observed only limited genetic variation within populations and taxa. Nevertheless, each studied individual exhibited a unique genotype. An analysis of molecular variance revealed high levels of genetic variation between taxa, but populations were genetically less different. The clear genetic differentiation between the studied taxa was supported by neighbor‐joining cluster analyses and principal coordinate analyses in which every individual was clearly assigned to its respective taxon. The three potentially new taxa were genetically as well differentiated as the other taxa included in our study. This supports the assumption that they should be treated as taxonomically independent units of high conservation interest. Therefore, the genetic analysis confirmed the morphologically based classification of the studied Hieracium taxa. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 112–123.     

Phylogenetic analysis,taxonomic revision,and dental ontogeny of the Cretaceous Zhelestidae (Mammalia: Eutheria)

Iphisa elegans Gray, 1851 is a ground‐dwelling lizard widespread over Amazonia that displays a broadly conserved external morphology over its range. This wide geographical distribution and conservation of body form contrasts with the expected poor dispersal ability of the species, the tumultuous past of Amazonia, and the previously documented prevalence of cryptic species in widespread terrestrial organisms in this region. Here we investigate this homogeneity by examining hemipenial morphology and conducting phylogenetic analyses of mitochondrial (CYTB) and nuclear (C‐MOS) DNA sequence data from 49 individuals sampled across Amazonia. We detected remarkable variation in hemipenial morphology within this species, with multiple cases of sympatric occurrence of distinct hemipenial morphotypes. Phylogenetic analyses revealed highly divergent lineages corroborating the patterns suggested by the hemipenial morphotypes, including co‐occurrence of different lineages. The degrees of genetic and morphological distinctness, as well as instances of sympatry among mtDNA lineages/morphotypes without nuDNA allele sharing, suggest that I. elegans is a complex of cryptic species. An extensive and integrative taxonomic revision of the I. elegans complex throughout its wide geographical range is needed. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 361–376.     

Conservation genetics of the rare Iberian endemic Cheirolophus uliginosus (Asteraceae)

Cheirolophus uliginosus is a rare species, endemic to the south‐western Iberian Peninsula, and listed as a characteristic taxon from the temperate Atlantic wet heaths, a priority habitat for conservation by the European Union. The conservation status of this species in most of its distribution area is poorly known, but, in recent times, some populations have disappeared and there has been a reduction in the number of individuals in others. In this context, we analysed the effects of population size on genetic diversity, revealing that genetic erosion and inbreeding depression could be having a significant impact on smaller populations. Furthermore, we studied the patterns of genetic structure and variability at the species level, finding a strikingly low within‐population diversity and high among‐population genetic differentiation. Finally, the genetic structure analyses suggested a long and complex phylogeographical history of C. uliginosus in the region, in agreement with the climate relict status proposed for this species. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 157–171.     

Process‐Based Species Action Plans: an approach to conserve contemporary evolutionary processes that sustain diversity in taxonomically complex groups

Many endemic plant species belong to taxonomically complex groups. These endemics have often arisen as a consequence of recent and rapid evolutionary divergence facilitated by processes such as hybridization, polyploidy and/or breeding system transitions. The rapid and dynamic nature of divergence in taxonomically complex groups leads to problems in the implementation of traditional species‐based approaches for the conservation of the biodiversity that they contain. Firstly, the taxa of interest can be difficult to define and identify, leading to practical difficulties in implementing conservation measures. Secondly, a species‐based approach often fails to capture the complexity of diversity present in the taxonomically complex group. To accommodate these challenges, we have developed a Process‐Based Species Action Plan approach. This is designed to conserve the processes leading to the generation of biodiversity, rather than focusing on the preservation of individual named taxa. We illustrate the approach using a group of endemic tree species (Sorbus) on the Scottish island of Arran that have originated via a combination of multiple recent hybridization events and apomixis. The plan focuses on the optimization of habitat management to ensure the reproduction and regeneration of Sorbus in the zone in which these evolutionary processes operate, and to facilitate hybridization that will ensure the continued generation of diversity in this group. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 194–203.     

Genetics,taxonomy and the conservation of British <Emphasis Type="Italic">Euphrasia</Emphasis>

In Britain the genus Euphrasia comprises ca 20 diploid and tetraploid plant species, including several endemics. However, their conservation is impeded by taxonomic uncertainty. Analysis of cpDNA and AFLP variation was used to assess their taxonomic status and establish the extent of barriers to gene exchange among them. Differences in ploidy level constitute a very strong barrier to genetic exchange, although this is not absolute. The diploid endemics E. vigursii and E. rivularis form morphologically and genetically definable units which show some level of reproductive isolation. Within tetraploid Euphrasia, the species showed varying degrees of distinctness. Analysis of geographically paired samples from two widespread outcrossing taxa E. arctica and E. nemorosa provides evidence for extensive genetic exchange between them. However AFLP data indicate that this outbreeding species complex possesses a gene pool distinct from that of the widespread inbreeding tetraploids. The widespread and endemic inbreeding tetraploids contain examples of morphologically and genetically definable taxa, but also species whose distinctness is more equivocal. The conservation implications of this study are that species-based action plans are potentially suitable for conservation of the diploid endemics E. vigursii and E. rivularis. In contrast we contend that a species-based conservation framework, developed with reproductively isolated and genetically distinct groups in mind, requires modification for conservation of the complex and dynamic diversity found within the tetraploids. The adoption of ‘taxonomic’ action plans, designed to protect the evolutionary processes generating Euphrasia diversity, may provide a supplementary solution for conserving this type of variation.     

High genetic and morphological diversity despite range contraction in the diploid Hieracium eriophorum (Asteraceae) endemic to the coastal sand dunes of south‐west France

Endemic plants inhabiting coastal sand dunes show augmented extinction risks due to the dynamic nature of dunes and strong human pressure on coastal areas. To investigate the survival strategies and threats to long‐term survival of such species, we combined genetic, morphological and biogeographical approaches, using the example of Hieracium eriophorum (Asteraceae) and its putative cryptic sister species H. prostratum, which are endemic to the longest coastal sand dune in Europe. An analysis of amplified fragment length polymorphism revealed high within‐population genetic variability, and slight isolation by distance was the only indication of genetic population structure. Thus, no signs of genetic threats to survival were found. Furthermore, genetic and morphometric data provided no evidence for the existence of two species. Therefore, we propose to synonymize H. prostratum with H. eriophorum and provide a nomenclatural overview with typification. Finally, an analysis of historical distribution records showed that, during the last 100 years, the species was lost from its range margins, where its habitat became fragmented. Taken together, our results suggest that one successful survival strategy of narrow endemics may be the achievement of large local population sizes on a small geographical scale, thus avoiding the genetic problems inherent to small and fragmented populations. Dune management policies should thus take care that the current tendencies to allow more erosion will not result in too severe fragmentation of the remaining continuous stretches of dune habitat. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169 , 365–377.     

Phylogeography and population differentiation in terrestrial island populations of Banksia arborea (Proteaceae)

The Banded Iron Formations (BIFs) of south‐western Australia are terrestrial islands characterized by high species richness and endemism. Regional endemics occur across multiple formations without inhabiting the intervening landscape matrix. We investigated whether the occurrence on BIF terrestrial islands has led to genetic differentiation among the eight known populations of the regional endemic, Banksia arborea. Genetic structure was assessed using three chloroplast DNA sequence markers and 11 nuclear microsatellite loci. Phylogenetic relationships were assessed with statistical parsimony and Bayesian methods. Dates of haplotype divergence were estimated using the time to most recent common ancestor of B. arborea and Banksia purdieana, as well as a conservative angiosperm chloroplast (cp)DNA mutation rate. Population genetic diversity and structure was assessed amongst and within populations by genotyping 24 geographically clustered individuals from each BIF and three subpopulations within the Die Hardy Range BIF. Indirect gene flow estimates were determined using a method based on the frequency of private alleles. Banksia arborea showed low genetic diversity in (cp)DNA and a complex structural pattern, with genetic differentiation of some BIF populations and an absence of differentiation amongst others, reflecting either retention of ancestral polymorphism across northern BIF populations or more recent connectivity of these populations. There was little evidence of pollen dispersal both between BIFs and within the large BIF known as Die Hardy Range. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 860–872.     

Patterns and traits of the endemic plants of Greece

Greece is characterized by high plant diversity (5800 species) and endemism (15.6%). This study attempts a first overall assessment of the taxonomy, distribution, traits and conservation status of the Greek endemic plants. The endemic species belong to 56 families and 242 genera. Most of the endemic plants have a narrow geographical and altitudinal distribution range. The southern floristic regions are richer in endemic species. The species area relationships for endemics (EARs) for island and continental floristic regions explain over 50% of the variation in number of species and are characterized by steep curves. Analysis of the distributional pattern of the endemics by similarity coefficients offers useful insights into the palaeogeography and biogeography of Greece. The endemic species occur at all altitudes, but the altitudinal distribution shows a predominance of local endemics at 0–600 m in the island regions and in higher zones in the continental regions. The life form spectra show a predominance of hemicryptophytes and chamaephytes. This trait seems indicative of their habitat and adaptive strategy and may be related to speciation processes. The overview of the conservation status of the Greek endemics indicates that over 40% of the taxa are threatened or near threatened. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 162 , 130–422.     

Phylogeography of palo santo trees (Bursera graveolens and Bursera malacophylla; Burseraceae) in the Galápagos archipelago

Two species of palo santo trees are distributed in the Galápagos archipelago, the native Bursera graveolens and the endemic Bursera malacophylla (Burseraceae). However, a zone of individuals morphologically intermediate between the two exists on northern Santa Cruz Island and south‐eastern Santiago Island, suggesting that they may not be reproductively isolated. Here we review the species' distributional and morphological differences and test for evidence of hybridization between the two species using DNA sequence and AFLP data. We find that the species lack distinguishing synapomorphies across the five nuclear and plastid regions examined. Population assignment tests and population genetic analyses of AFLP data indicate that genetically similar palo santo individuals (N = 87), including putative hybrids, partition into two genealogical groups that do not uniformly correspond to island‐ or taxon‐based membership. Furthermore, genotypic admixture levels among morphologically intermediate individuals do not indicate widespread hybridization. Thus, we recommend recognizing the endemic palo santo taxon as B. graveolens subspecies malacophylla (B.L.Rob.) A. Weeks & Tye comb. & stat. nov. in light of its close genetic relationship to B. graveolens subsp. graveolens and its distinctive morphology and distribution. Future research should quantify phenotypic variation in palo santo populations as another means for understanding the basis of morphological differences between the subspecies. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 161 , 396–410.     

Cytogenetic and molecular characterization of morphologically variable Sisyrinchium micranthum (Iridaceae) in southern Brazil

Sisyrinchium micranthum is native to southern Brazil and shows a wide range of morphological variation in this region. This study was performed to compare individuals of this species in terms of traits such as morphology, chromosome number, meiotic behaviour, pollen viability and genetic diversity using inter simple sequence repeat markers. First, general morphological aspects were evaluated and plants were classified into three morphological categories (CI, CII and CIII) to analyse the cytogenetic and genetic data. Three chromosome numbers corresponding to three ploidies were found: 2n = 2x = 16, 2n = 4x = 32 and 2n = 6x = 48. All morphological types showed regular meiotic behaviour and high meiotic index values and pollen viability. CII is the most frequent in southern Brazil. The most common haploid chromosome number, n = 8, has not been reported previously in this species. The percentage of polymorphic loci ranged from 6.45 to 61.29% for each accession. Molecular and cytogenetic analyses indicate that some S. micranthum accessions may have more than one ploidy. This study represents the first effort to characterize this taxonomically complex species based on cytogenetic and genetic aspects. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169 , 350–364.     

A multigene molecular assessment of cryptic biodiversity in the iconic freshwater blackfishes (Teleostei: Percichthyidae: Gadopsis) of south‐eastern Australia

Freshwater biodiversity is under ever increasing threat from human activities, and its conservation and management require a sound knowledge of species‐level taxonomy. Cryptic biodiversity is a common feature for aquatic systems, particularly in Australia, where recent genetic assessments suggest that the actual number of freshwater fish species may be considerably higher than currently listed. The freshwater blackfishes (genus Gadopsis) are an iconic group in south‐eastern Australia and, in combination with their broad, naturally divided distribution and biological attributes that might limit dispersal, as well as ongoing taxonomic uncertainty, they comprise an ideal study group for assessing cryptic biodiversity. We used a multigene molecular assessment including both nuclear (51 allozyme loci; two S7 introns) and matrilineal markers (cytb) to assess species boundaries and broad genetic substructure within freshwater blackfishes. Range‐wide examination demonstrates the presence of at least six candidate species across two nominal taxa, Gadopsis marmoratus and Gadopsis bispinosus. Phylogeographical patterns often aligned to purported biogeographical provinces but occasionally reflected more restricted and unexpected relationships. We highlight key issues with taxonomy, conservation, and management for a species group in a highly modified region. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 521–540.     

Comparative biogeography reveals differences in population genetic structure of five species of stream fishes

The distribution of genetic variation in Texas stream fishes has been shaped by a complex mix of historical and anthropogenic factors. Although Texas was not glaciated during the Pleistocene, the rise in sea level following this epoch isolated formerly connected drainages. More recently, the construction of dams, modifications of stream systems, and the release of commercially raised fish have influenced the patterns of genetic diversity. To examine how these different factors have impacted Texas stream fishes, we compared the genetic structure of five species of fish spanning two families and inhabiting two adjacent drainages: Lepomis megalotis, Lepomis cyanellus, Cyprinella lutrensis, Cyprinella venusta, and Campostoma anomalum. Our analyses of the mitochondrial D‐Loop show that genetic patterns differ strongly across species. A phylogeographical split between the Brazos and Trinity drainages was seen in conspecific populations of Lepomis species and is probably the result of the historical separation of these river systems. In contrast, contemporary ecological and anthropogenic factors, such as the desiccation of streams during summer, and the translocation of bait fish, appear to have a stronger influence on the genetic patterns in the remaining species. The contrasting results demonstrate the importance of using a multi‐species, comparative approach for landscape genetic studies as single species patterns may not be representative of others and thus may obscure differential effects of historical versus recent events as well as natural versus anthropogenic forces. By comparing closely related species that differ in their life history and economic importance it may be possible to disentangle the relative roles of historical, intrinsic, and anthropogenic influences on different organisms within a region. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

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.     

A second species in the endemic New Caledonian genus Gastrolepis (Stemonuraceae) and its implications for the conservation status of high‐altitude maquis vegetation: coherent application of the IUCN Red List criteria is urgently needed in New Caledonia

A new species in the previously monotypic, endemic New Caledonian genus Gastrolepis (Stemonuraceae) is described. Gastrolepis alticola differs from G. austrocaledonica by its shorter and thicker petioles, strongly coriaceous leaves with revolute margins, shorter inflorescences, and pubescent corollas. The new species is further distinguished by its ecology, occurring only in high‐altitude maquis on two massifs in southern New Caledonia, Mt. Kouakoué and the Montagne des Sources. Gastrolepis alticola is assigned a preliminary conservation status of ‘Endangered’ using the World Conservation Union (IUCN) Red List criteria. Comparison of the IUCN threat status for the 19 species endemic to this distinctive, restricted vegetation type reveals a striking lack of consistency and underscores the need for a reassessment of the entire New Caledonian flora. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 157 , 775–783.     

The subspecies concept in butterflies: has its application in taxonomy and conservation biology outlived its usefulness?

Subspecies lie at the interface between systematics and population genetics, and represent a unit of biological organization in zoology that is widely used in the disciplines of taxonomy and conservation biology. In this review, we explore the utility of subspecies in relation to their application in systematics and biodiversity conservation, and briefly summarize species concepts and criteria for their diagnosis, particularly from an invertebrate perspective. The subspecies concept was originally conceived as a formal means of documenting geographical variation within species based on morphological characters; however, the utility of subspecies is hampered by inconsistencies by which they are defined conceptually, a lack of objective criteria or properties that serve to delimit their boundaries, and their frequent failure to reflect distinct evolutionary units according to population genetic structure. Moreover, the concept has been applied to populations largely comprising different components of genetic diversity reflecting contrasting evolutionary processes. We recommend that, under the general lineage (unified) species concept, the definition of subspecies be restricted to extant animal groups that comprise evolving populations representing partially isolated lineages of a species that are allopatric, phenotypically distinct, and have at least one fixed diagnosable character state, and that these character differences are (or are assumed to be) correlated with evolutionary independence according to population genetic structure. Phenotypic character types include colour pattern, morphology, and behaviour or ecology. Under these criteria, allopatric subspecies are a type of evolutionarily significant unit within species in that they show both neutral divergence through the effects of genetic drift and adaptive divergence under natural selection, and provide an historical context for identifying biodiversity units for conservation. Conservation of the adaptedness and adaptability of gene pools, however, may require additional approaches. Recent studies of Australian butterflies exemplify these points. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.