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The General Lineage Concept of Species, Species Criteria, and the Process of Speciation: A Conceptual Unification and Terminological Recommendations
... It has not been a common practice to explicitly express our views of organismic species in individual empirical taxonomic papers of rust (and/or other) fungi. Almost insurmountable disagreements between different species concepts and recognition criteria come from different views or philosophy as to how the separately evolving lineages arise and how they can be appropriately delimited and recognized (e.g., Agapow et al., 2004;de Queiroz, 1998;Harrison, 1998;Hull, 1999;Mayden, 1997). Organisms exhibit a great diversity of biological properties, that we have not yet well understood and accurately evaluated. ...
... Organisms exhibit a great diversity of biological properties, that we have not yet well understood and accurately evaluated. Different biological properties evolve neither in regular sequence nor tempo among different organisms (de Queiroz, 1998(de Queiroz, , 2007. Therefore, no single concept and criterion can suffice to recognize species. ...
... Nonetheless, explicit, even simple and brief, statement or interpretation as to how species is recognized in each empirical study would be beneficial to make proper evaluation of the species recognition and their classification by different authors, who might have distinct philosophy about species. My view of rust species and methods to delimit them follow the theoretical and practical considerations of the species concept and species recognition by Avise and Wollenberg (1997), A d v a n c e P u b l i c a t i o n de Queiroz (1998de Queiroz ( , 1999de Queiroz ( , 2007, Freudenstein et al. (2017), Mayr (1982Mayr ( , 1988, Ono (2000Ono ( , 2008, and Ono et al. (2020b). Theoretically, species exist as a separately evolving metapopulation lineage (de Queiroz, 1998(de Queiroz, , 1999(de Queiroz, , 2007. ...
Rust species classified in Ochropsora, Aplopsora, and Cerotelium pro parte were re-examined and re-circumscribed by morphology, host preference, life cycle pattern, and geographic distribution. Macrocyclic heteroecious life cycle was proven for seven species by field observations and experimental inoculations. Partial molecular phylogenetic analyses were also included in the taxonomic decision. Anamorphic fungi and others, that were newly discovered and assumed to be related to these genera, were also examined in the same manner. Aplopsora was synonymized under Ochropsora. One fungus named under Cerotelium and two anamorphic fungi were determined as species of Ochropsora. Fifteen species were recognized in Ochropsora: O. ariae, O. asari, O. asiatica, O. corni, O. cumminsii, O. ehimensis, O. dicentrae, O. kraunhiae, O. laporteae, O. lonicerae, O. nambuana, O. nyssae, O. panacis, O. staphyleae, and O. tanakae. Most of Ochropsora species are distributed in eastern Asia. Only O. ariae is known in northwestern Europe and O. cumminsii, O. dicentrae, and O. nyssae are known in eastern North America. The disjunct distribution of Ochropsora in the Northern Hemisphere is interpretated by disjunctions of ancestral species once broadly distributed in the Northern Hemisphere and subsequent species diversification, migration, and extinction in each of the three geographic regions.
... Internal transformation of a single species or dividing a single species into two peripheral species initiates the speciation (Mayr, 1963). Species are metapopulations exchanging their alleles frequently to the same gene pool, they tend to evolve seperately (de Queiroz, 1998(de Queiroz, , 1999. ...
... has not claimed and the definitions are still remaining uncertain (Charles Darwin, 2004;de Queiroz, 1998de Queiroz, , 1999Mayr, 1940;Schluter, 2001;Wheeler & Meier, 2000). ...
... With the drawbacks of Mayr's biological species concept, a new theory comes to the stage defining the species as separately evolving metapopulations which can exchange their alleles frequently to the same gene pool (de Queiroz, 1998(de Queiroz, , 1999. ...
Kentish plover (Charadrius alexandrinus) complex is a superspecies consisting several closely related metapopulations from different geographical locations. Charadrius alexandrinus seebohmi found in Sri Lanka and south-east India are considered as a subspecies of Kentish plover complex since 1915. This subspecies variation was justified under breeding plumage of adult male C. a. seebohmi. My study was aimed to investigate the genetic and phenotypic differentiation between C. a. seebohmi and nominated migrant C. a. alexandrinus. Several biometrics and different breeding plumage characters were used in phenotypic analysis and four genetic markers; partial mitochondrial d-loop control region (CR), NADH dehydrogenase subunit 3 (ND3) and two z chromosome linked loci (Z4 and Z45) and eleven microsatellite markers were used to assess the gene flow of C. a. seebohmi among other closely related taxa. Following a species delimitation criterion, C. a. seebohmi uplifted its taxonomic status to a complete species. In addition, C. a. seebohmi is rather smaller entity with a shorter wing suggesting its resident breeding status compared to the longer wing of C. a. alexandrinus. Since C. seebohmi is sexually dimorphic, clarity and the size of front eye-lore can be used as a measurement to elaborate its gender. Bayesian cluster analysis revealed C. seebohmi’s genetic isolation from other closely related taxa. Bayesian and Maximum likelihood (ML) approaches for reclassifying the phylogenetic tree for a subset of Charadrius plovers suggest C. seebohmi’s taxonomic position fixed to the clade of C. alexandrinus. ML based divergence time estimations resulted in an approximation of nearly a million ago (1.1 MYA) divergence time for C. seebohmi and C. alexandrinus. However, the mode of speciation is quite unclear whether its allopatric or parapatric. As a conclusion, both phenotypic and genetic isolation of C. seebohmi suggest its taxonomic status as a full species under General Lineage Concept (GLC) of species.
... Here we broadly adopt the general lineage conception of species (de Queiroz 1998(de Queiroz , 2007, in which species are time-extended lineages that are evolving independently of one another. Under this view, attributes that have formally been viewed as necessary and sufficient defining criteria for species (e.g., reproductive isolation, ecological differentiation, or reciprocal monophyly), are instead understood to provide evidence bearing on whether, in fact, two lineages are evolving separately. ...
... Focusing first on monophyly, three of the alternatives would yield one or more paraphyletic sets of populations, which together do not form a "historically sufficient unit" (sensu Maddison and Whitton, 2023): C1-6 under alternative (1), C1-3 and C4-6 under alternative (3), and C2-6 under alternative (4). It might be argued that monophyly is unexpected, and is an unnecessary criterion, in such a recent progenitor/derivative relationship-the observed phylogenetic nestedness is simply the expected outcome of the differentiation of a peripheral set of populations (e.g., Rieseberg and Brouillet 1994;Olmstead 1995;Chandler and Crisp 1996;de Queiroz 1998). It is tempting to suppose that reciprocal monophyly would be the eventual outcome under these circumstances (Neigel and Avise 1986;Avise and Ball 1990;Rieseberg and Brouillet 1994). ...
... This may be more likely, but we think it even more probable that the now scattered populations will simply continue to diverge from one another with little interaction in the future. To be clear, in keeping with the general lineage concept of species (de Queiroz 1998(de Queiroz , 2005, we do not require that young or emerging species be monophyletic. And, if the paraphyletic progenitor populations showed signs of connectedness through gene flow, or if we predicted the eventual attainment of reciprocal monophyly, we might treat this case differently (Donoghue 2022). ...
A fundamental objective of evolutionary biology is to understand the origin of independently evolving species. Phylogenetic studies of species radiations rarely are able to document ongoing speciation; instead, modes of speciation, entailing geographic separation and/or ecological differentiation, are posited retrospectively. The Oreinotinus clade of Viburnum has radiated recently from north to south through the cloud forests of Mexico and Central America to the Central Andes. Our analyses support a hypothesis of incipient speciation in Oreinotinus at the southern edge of its geographic range, from central Peru to northern Argentina. Although several species and infraspecific taxa of have been recognized in this area, multiple lines of evidence and analytical approaches (including analyses of phylogenetic relationships, genetic structure, leaf morphology, and climatic envelopes) favor the recognition of just a single species, V. seemenii. We show that what has previously been recognized as V. seemenii f. minor has recently occupied the drier Tucuman-Bolivian forest region from Samaipata in Bolivia to Salta in northern Argentina. Plants in these populations form a well-supported clade with a distinctive genetic signature and they have evolved smaller, narrower leaves. We interpret this as the beginning of a within-species divergence process that has elsewhere in the neotropics resulted repeatedly in Viburnum species with a particular set of leaf ecomorphs. Specifically, the southern populations are in the process of evolving the small, glabrous, and entire leaf ecomorph that has evolved in four other montane areas of endemism. As predicted based on our studies of leaf ecomorphs in Chiapas, Mexico, these southern populations experience generally drier conditions, with large diurnal temperature fluctuations. In a central portion of the range of V. seemenii, characterized by wetter climatic conditions, we also document what may be the initial differentiation of the leaf ecomorph with larger, pubescent, and toothy leaves. The emergence of these ecomorphs thus appears to be driven by adaptation to subtly different climatic conditions in separate geographic regions, as opposed to parapatric differentiation along elevational gradients as suggested by Viburnum species distributions in other parts of the neotropics.
... Delineating subspecies taxonomically is debated by academics and agency personnel (Wilson and Brown 1953;de Queiroz 2020;Hillis 2019Hillis , 2020Burbrink et al. 2022). At its heart, the subspecies debate focuses on where, and whether, we draw the line between geographically distinct morphological variants (subspecies, as originally described in Mayr [1969]), and evolutionarily distinct lineages (species under the unified evolutionary species framework (de Queiroz 1998(de Queiroz , 2007. Given that the ESA explicitly protects subspecific units, either as subspecies or distinct populations (USFWS and NMFS 1996), our definitions of subspecies affects conservation efforts. ...
... Delineating subspecies taxonomically is debated by academics and agency personnel (Wilson and Brown 1953;de Queiroz 2020;Hillis 2019Hillis , 2020Burbrink et al. 2022). At its heart, the subspecies debate focuses on where, and whether, we draw the line between geographically distinct morphological variants (subspecies, as originally described in Mayr [1969]), and evolutionarily distinct lineages (species under the unified evolutionary species framework (de Queiroz 1998(de Queiroz , 2007. Given that the ESA explicitly protects subspecific units, either as subspecies or distinct populations (USFWS and NMFS 1996), our definitions of subspecies affects conservation efforts. ...
... We do not believe that monophyly or independent lineages (Nikolakis et al. 2022) should be expected for subspecific units, as other researchers have reported (Mikles et al. 2020, Marshall et al. 2021) and as theory predicts (Wilson and Brown 1953, Dufresnes et al. 2023. If subspecific lineages were truly independent, they might be better referred to as species, not subspecies (Wiley 1978;de Queiroz 1998de Queiroz , 2020Hillis 2020;Dufresnes et al. 2023). Rather, these sublineages necessarily show ongoing admixture, even if they were once historically isolated. ...
Whether or where to draw subspecies' taxonomic boundaries is much more than an esoteric argument. Subspecific taxonomies and associated geographic ranges have important conservation and management implications because the Endangered Species Act (ESA) protects distinct populations segments below the species level. Genomic data can help resolve taxonomic disputes and assist with conservation policy; however, because subspecific lineages often exhibit gene flow, genomic lineages for subspecific taxa are rarely distinct. We used genomic data from the eastern pinesnake ( Pituophis melanoleucus ) to determine the geographic range of the morphologically variable Florida pinesnake ( P. m. mugitus ), which is petitioned for listing under the ESA. The overall genomic pattern of the eastern pinesnake is one of admixture, and there are gradual differences over the wide range of the species. But there still are discernable areas of genetic differentiation that correspond to the morphologically defined Florida pinesnake, and other subspecies. This pattern of admixture should be expected for subspecies. We propose that boundaries for the Florida pinesnake should maximize the species redundancy, resilience, and representation based on genomic data. We also propose best practices for managers and policymakers interpreting genomic data of subspecies, given that the genomic cutoffs will rarely be truly distinct.
... Species delimitation requires multiple sources of evidence (de Queiroz, 1998(de Queiroz, , 2007Dayrat, 2005), and novel technologies that are both fast and inexpensive, along with analytical advances, have significantly enhanced the effectiveness and precision of species delimitation (Bik, 2017). Leaf spectra have been used to accurately discriminate taxa at different taxonomic levels (e.g., Durgante et al., 2013;Lang et al., 2017;Vasconcelos et al., 2020aVasconcelos et al., , 2021Gaem et al., 2022). ...
... Species concept. We adopted the unified species concept proposed by de Queiroz (1998Queiroz ( , 2007, in which species are regarded as metapopulation lineages that evolve separately from one another. Under this definition, lineages that are morphologically distinct, but not necessarily monophyletic or reproductively isolated, may be regarded as species, depending on the criteria and methods used to make such inferences. ...
Ecclinusa guianensis (Sapotaceae, Chrysophylloideae) is a morpho-ecologically variable species and the second most widespread species of Ecclinusa in the Amazon basin. In Central Amazonia, two distinct leaf morphotypes can be field-recognized based on diagnostic morphology: elliptic-obovate and narrow-oblanceolate shapes. In this paper, we have explored the phenotypic differentiation between these two morphotypes of E. guianensis from Central Amazonia using morphometrics and near-infrared spectroscopy data. The results indicate the existence of two distinct groups that are sympatric. However, the narrow-oblanceolate leaf shape (subcanopy treelets or medium-sized trees) has never been collected with reproductive material, reinforcing the idea that it is a young phase of the elliptic-obovate leaf shape (large canopy trees). Therefore, we presume that Ecclinusa guianensis morphotypes probably correspond to a single species exhibiting phenotypic plasticity.
... For this purpose, morphometric methods allow the assessment of the phenotypic variation between species with unclear separation, and potentially can indicate the differences in terms of size and shape (Pinheiro et al. 2018, Sokal & Michener 1958. A species complex can be defined as closely related species that present difficulties for morphological circumscription because intricate patterns of morphological, genetic and ecological variation (Pinheiro et al. 2018, de Queiroz 1988. Morphometric methods have often been applied to species complexes in the orchid family, in order to better assess species delimitation (e.g. ...
... Overall species delimitation:-From the various species concepts applied to plants (de Queiroz 1988, Templeton 1989, De Queiroz 2005, de Queiroz 2007, Aleixo 2009, Pinheiro et al. 2018, Fišer 2018, we decided to apply the cohesion species concept of Templeton (1989), where a species is represented by the largest group of individuals that have competence of phenotypic cohesion through intrinsic resources of cohesion. With this concept in mind, we use our morphometric approach to enable a morphological species circumscription within the species complex in the present study. ...
In the present study we perform a linear morphometric analysis to assess species delimitation in Cattleya caulescens, C. pabstii, and C. pfisteri, which constitute a species complex in Brazilian campos rupestres. For this purpose, we collected 18 linear measurement variables from flowers of 153 individuals in 11 populations from the three species in the Brazilian States of Minas Gerais and Bahia. We applied Principal Component Analysis (PCA), Canonical Variate Analysis (CVA) and cluster analysis to assess the morphological variation between populations. The analyses indicated a clear difference and cohese clusters of populations for each species, but one of the populations of C. pfisteri was divergent from the other populations. This difference is putatively explained by genetic data from other studies that suggest introgression from a species from a different series, C. sincorana, in this location. The differences between C. caulescens and C. pabstii reinforce the floristic differentiation of the orchid flora from the quartzitic mountains of Southern Minas Gerais in relation to the Espinhaço range to the north, as well as the development of a specialized orchid flora in the iron ore outcrops in Central Minas Gerais.
... The Lineage Species Concept [34] was chosen for species delimitation as an effective consensus. Reciprocal monophyly of lineages was used as an obligatory species delineation criterion [34]; morphological diagnosability [35,36] and host-specificity [37] were considered as additional evidence. ...
... The Lineage Species Concept [34] was chosen for species delimitation as an effective consensus. Reciprocal monophyly of lineages was used as an obligatory species delineation criterion [34]; morphological diagnosability [35,36] and host-specificity [37] were considered as additional evidence. ...
... There is today widespread agreement that species delimitation should be treated as a hypothesis-testing exercise (de Queiroz 1998, Padial et al. 2010, Puillandre et al. 2012, Miralles et al. 2024, where species are defined as independently evolving metapopulation lineages and criteria for species delimitation must be firmly established. The hypothesis that a biological entity constitutes a species, derived from morphological differences or a distinct mtDNA haplotype clade, can then be tested using additional evidence or alternative approaches (Padial et al. 2010). ...
... This statement is problematic because (1) on an operational level, it confuses gene tree and species tree: just because a mitochondrial tree suggests paraphyly, it does not necessarily follow that the same is true for the underlying evolutionary relationships among lineages, especially considering the possibility of phenomena such as introgression or incomplete lineage sorting (e.g. Marshall et al. 2021); (2) on a conceptual level, there is no need at all for a species to be monophyletic: a species is a segment of a population lineage that does not equal a clade (de Queiroz 1998, Hillis 2022, Vences et al. 2024; and (3) recognition of a subspecies cannot make a species paraphyletic, only potentially one of the other subspecies of that species. ...
A recent revision of the anacondas (Serpentes: Boidae: Eunectes), with the description of a new species of green anaconda, generated extensive publicity, but also provoked considerable controversy due to inadequacies of the evidence used and errors in nomenclature. We here use the case of this problematic publication to: (i) highlight common issues affecting species delimitations, especially an over-reliance on mitochondrial DNA data, and reiterate best practices; (ii) reanalyse the data available for anacondas to establish the true current state of knowledge and to highlight lines of further research; and (iii) analyse the nomenclatural history and status of the genus. While our analysis reveals significant morphological variation in both green and yellow anacondas, denser sampling and an analysis of informative nuclear markers are required for meaningful species delimitation in Eunectes. Tracing the history of name-bearing types establishes Trinidad as the type locality for Boa murina Linnaeus, 1758 and allows identification of the extant lectotype for the species. Finally, we emphasize the responsibility of both journals and authors to ensure that published taxonomic work meets the burden of evidence required to substantiate new species descriptions and that species are named in compliance with the rules of zoological nomenclature.
... only three individuals of pincoyae were assigned to chilensis, one individual of chilensis was assigned to exasperatus, and two individuals of oceanicus were assigned to barrosi and two others to exasperatus, respectively (Fig. S3, Table S2). Based on our phylogenetic hypothesis and morphological analyses, and following the general lineage species concept (hereafter glSC; de Queiroz 1998de Queiroz , 1999de Queiroz , 2007 and the International Code of zoological Nomenclature (ICzN 1999), we here propose the recognition of the Oceanites population of central Chile as a new taxon: ...
... We included specimens sampled close to type localities and a broad representation of biometric data from museums. our sampling suggests that each formerly described subspecies must be elevated to a species category following the glSC (de Queiroz 1998(de Queiroz , 1999(de Queiroz , 2007. our results show that subspecies within two of the currently recognized Oceanites species are polyphyletic. ...
The family oceanitidae, formerly considered a subfamily of Hydrobatidae, includes all the small storm-petrels of the southern hemisphere. The ancestor-descendent relationships and evolutionary history of one of its genera, Oceanites, have been partially studied, yielding contrasting results. We revised the phylogenetic relationships of this group using Bayesian inference (BI) based on new sequence data of the mitochondrial gene Cytb and linear morphological measurements of all species and five subspecies-level taxa in Oceanites, including a new taxon from the Chilean Andes. our BI results show that the Oceanites genus is monophyletic and composed of four well-supported clades (posterior probability > 0.95): (1) chilensis; (2) exasperatus; (3) gracilis, pincoyae, and barrosi sp. nov.; and (4) oceanicus and galapagoensis. The species O. chilensis is a basal clade within Oceanites. According to our time-calibrated tree, the split between Oceanites and the other genera in Family oceanitidae is estimated to be ~35.9 Mya, and the oldest divergence within Oceanites (the split between O. chilensis and other Oceanites) was dated to the early Miocene, around c. 21.3 Mya. The most probable geographic origin of Oceanites is the Southern ocean. The morphological data suggest continuous size variation between Oceanites taxa, ranging from smallest in gracilis to largest in exasperatus. Based on our phylogenetic hypothesis, and morphological analyses, we suggest elevating to species status the taxa galapagoensis, chilensis, and exasperatus, and we describe a new taxon barrosi sp. nov., thus recognizing a total of seven species within the genus Oceanites.
... The existence of myriad species concepts (Mayden 1997;de Queiroz 1998) and active debate over species delimitation (cf. Chambers and Hillis 2020;Burbrink and Ruane 2021) is sometimes framed as problematic. ...
... In recent years, discussion about species has shifted away from species concepts to the means of identifying species-level lineages (de Queiroz 1998;Hillis et al. 2021). Advances in genomics have greatly increased the amount of data available to the average study, while computational improvements have addressed the problem of demarcating evolutionary groups. ...
Abstract:
Species are the fundamental unit of biodiversity studies. However, many species complexes are difficult to delimit, especially those characterized by complicated patterns of population structure. Salamanders in the family Plethodontidae often form species by slowly fragmenting across a landscape over space and time. They thus provide many examples of species complexes in which gradual Darwinian evolution has resulted in multiple units of varying degrees of differentiation, including incompletely separated lineages. Herein, we report on a molecular systematic investigation of woodland salamanders in the Plethodon wehrlei group, a group that has recently been split from two species into five species. To quantify patterns of genetic variation, we collected genetic samples from 24 individuals from 20 populations, including all species and representing a carefully selected subset of previous work. From these samples, we obtained genomic data by using anchored hybrid enrichment, resulting in 319 loci averaging 1300 bp in length. Biallelic single-nucleotide polymorphisms were randomly selected from 316 of these loci for some analyses. We examined patterns of genetic structure by using a combination of multivariate statistics and methods based on evolutionary models (such as the Bayesian program STRUCTURE) and found that all of the recognized species formed genetic clusters; however, P. wehrlei and P. punctatus were relatively weakly differentiated and STRUCTURE identified three separate clusters within P. jacksoni. Species trees inferred using the weighted accurate species tree algorithm (wASTRAL), Bayesian phylogenetics and phylogeography (BPP), and TreeMix all recovered the same topology, with P. dixi sister to the other taxa, which included a northern clade (P. wehrlei, P. punctatus, P. pauleyi) and a southern clade (P. jacksoni, with three separate groups). TreeMix only inferred one gene flow event. We evaluated the candidate species by using BPP and the genealogical divergence index (gdi). Although BPP delimited all candidate species with strong support (all posterior probabilities = 1.0), the gdi only strongly supported P. dixi and P. pauleyi, both of which have only been recently described. We discuss the difficult problem of species delimitation in groups that form species via range fragmentation. We also provide a vision for future research, with the aim of better testing and diagnosing the species diversity within the P. wehrlei group.
... Evolutionary proccesses tend to create continuous variation (Darwin 1859), which presents difficulties for those attempting to fit categorical classification schemes to organisms (de Queiroz 1998;Remsen 2010). Occasional or ongoing introgression between lineages is now known to be common, and hence the condition of complete reproductive separation among lineages is not as ubiquitous as once thought under the biological species concept (Jackson et al. 2017;Wang et al. 2019;de Queiroz 2020;Pulido-Santacruz et al. 2020). ...
... While modern biologists have increasingly found consensus in the broad concept that species are segments of population-level evolutionary lineages, the existence of incomplete lineage separation creates 'gray zones' in speciation. As a result, there is considerable debate regarding where the limits between species should be drawn (de Queiroz 1998;Burbrink et al. 2022). ...
The subspecies rank has been widely applied by taxonomists to capture infraspecific variation within the Linnaean classification system. Many subspecies described throughout the 20 th century were recognised largely based on perceived variation in single morphological characters yet have since been found not to correspond to separately evolving population lineages, thus requiring synonymy or elevation to full species under lineage-based views of species. These modern lineage-based taxonomic resolutions have resulted from a combination of new molecular genetic techniques, improved geographical sampling of specimens, and more sophisticated analyses of morphological variation (e.g., statistical assessments rather than solely univariate descriptive ones). Here, we revisit the current taxonomic arrangement of species-level and subspecific taxa in the Lerista microtis (Gray) group, which is distributed along a narrow ~2000 km strip on the southern coast of Australia. From specimens of the L. microtis group, an additional species (Lerista arenicola) and two additional subspecies (L. m. intermedia and L. m. schwaneri) were described. We collected data on mensural, meristic, and colour pattern characters to explore morpho-spatial relationships among these taxa. Although our morphological analyses revealed some distinctiveness among specimens from locations assigned to each taxon, this variation is continuous along Australia's southern coastline, assuming the form of a geographic cline rather than discrete forms. For many characters, however, spatial patterns were inconsistent with the original descriptions, particularly of the subspecies. Moreover, analysis of genome wide restriction-associated DNA loci revealed multiple instances of paraphyly among taxa, with phylogenetic clustering of specimens assigned to distinct species and subspecies. These emerging patterns provide no support for L. arenicola as a species evolving separately from L. microtis. Additionally, our findings challenge the presumed distinctiveness and coherence of the three subspecies of L. microtis. We thus synonymise L. arenicola and the L. microtis subspecies with L. microtis and provide a redescription of a single yet morphologically variable species-an arrangement that best reflects evolutionary history and the continuous nature of morphological variation across space.
... In our taxonomic revisionary papers on southern hemisphere Myosotis and here, we have used the general-lineage species concept (de Queiroz, 2007;de Queiroz, 1998) to delimit species as separately evolving lineages, where possible using multiple lines of evidence in an integrative framework (e.g., Meudt, 2021Meudt, , 2017Meudt et al., 2013;Prebble et al., 2022). In addition, we have used subspecies rank for allopatric taxa that have few minor distinguishing characters that may have limited overlap (Stuessy 2009;Meudt 2021). ...
... Despite considerable progress in achieving a more unified concept of species (Mayden 1997;de Queiroz 1998de Queiroz , 2007Hey 2006), the empirical application of such a concept presents challenges, particularly in cases of recent and/or incomplete divergence (e.g., de Queiroz 2005a, Carstens et al. 2013, Jackson et al. 2017. The Galapagos giant tortoises represent such a case. ...
Galapagos giant tortoises are endemic to the Galapagos Archipelago, where they are found in isolated populations. While these populations are widely considered distinguishable in morphology, behavior, and genetics, the recent divergence of these taxa has made their status as species controversial. Here, we apply multispecies coalescent methods for species delimitation to whole genome resequencing data from 38 tortoises across all 13 extant taxa to assess support for delimiting these taxa as species. In contrast to previous studies based solely on divergence time, we find strong evidence to reject the hypothesis that all Galapagos giant tortoises belong to a single species. Instead, a conservative interpretation of model-based and divergence-based results indicates that these taxa form a species complex consisting of a minimum of 9 species, with most analyses supporting 13 species. There is mixed support for the species status of taxa living on the same island, with some methods delimiting them as separate species and others suggesting multiple populations of a single species per island. These results make clear that Galapagos giant tortoise taxa represent different stages in the process of speciation, with some taxa further along in that evolutionary process than others. Our study provides insight into the complex process of speciation on islands, which is urgently needed given the threatened status of island species around the world.
Las tortugas gigantes de las Galápagos son endémicas del Archipiélago de Galápagos, donde se encuentran como poblaciones aisladas. Aunque estas poblaciones se consideran distinguibles en cuanto a morfología, comportamiento y genética, la divergencia reciente de estos taxones hace que su estatus como especies sea controvertido. Aquí aplicamos métodos de coalescencia de especies múltiples con datos de resecuenciación de genomas completos de 38 tortugas de los 13 taxones existentes para evaluar el sustento de la delimitación de estos taxones como especies. En contraste con estudios previos basados únicamente en el tiempo de divergencia, encontramos evidencia sólida para rechazar la hipótesis de que todas las tortugas gigantes de las Galápagos pertenecen a una sola especie. En cambio, una interpretación conservadora de los resultados basados en modelos y divergencia indica que estos taxones forman un complejo de especies que consiste de un mínimo de 9 especies, con la mayoría de los análisis respaldando la existencia de 13 especies. Hay sustento mixto para designar como especies a los taxones que habitan la misma isla, con algunos métodos delimitándolos como especies y otros sugiriendo la existencia de poblaciones múltiples de una sola especie por isla. Estos resultados dejan en claro que los taxones de tortugas gigantes de las Galápagos representan diferentes etapas del proceso de especiación, con algunos taxones más avanzados en ese proceso evolutivo que otros. Nuestro estudio ofrece una perspectiva sobre el complejo proceso de especiación en islas, la cual es urgentemente necesaria dado lo amenazadas que se encuentran las especies insulares en todo el mundo.
... I focus primarily on sexually reproducing species. Many species concepts concur that genetic exchange among conspecifics is an important aspect of species, including the biological (Wright 1940, Mayr 1942, Dobzhansky 1950, evolutionary (Simpson 1951, Wiley 1978, and general lineage concepts (de Queiroz 1998(de Queiroz , 2007. These three concepts are the most widely used (Stankowski and Ravinet 2021). ...
Speciation is the original source of all species richness. Here, I address two questions: (i) what might typical speciation look like across life? and (ii) how has speciation led to the diversity of life we see today? What is 'typical' depends on the richness of different groups. In groups associated with host organisms (which may dominate numerically), the processes of co-speciation and host switching are crucial. Among free-living organisms, allopatric speciation, ecological divergence, and prezygotic isolation appear widely important. Yet, the processes by which species become allopatric (and initially split) remain highly unclear. Among macroscopic organisms, the processes underlying the speciation of cryptic insect lineages may predominate, and are briefly reviewed here. Analyses of diversification rates among clades can illuminate the factors that drive speciation and species richness, and I review the advantages and disadvantages of different methods for estimating diversification rates. Patterns of species richness among named clades are generally related to variation in diversification rates, and specific types of ecological variables seem to underlie variation in diversification rates at different scales. Nevertheless, many richness patterns are unrelated to diversification rates and may be related to the time available for speciation instead, including richness among regions, clades, and traits.
... We followed the general lineage or unified species concept (de Queiroz, 1998(de Queiroz, , 2007, according to which a highly corroborated hypothesis of existence of a separate species requires multiple lines of evidence. We present phenotypic data (i.e., morphological features, color patterns), which corroborate the hypothesis of a new species of Erythrolamprus presented by Torres-Carvajal and Hinojosa (2020) based on phylogenetic relationships and genetic distances. ...
... A key principle of the integrative taxonomy framework is the recognition that species are lineages of individuals, where an ancestral lineage splits into 2 descendant species (de Queiroz 1998). Depending on the point in time along the speciation continuum and the type of datum examined, the descendant species may or may not show evidence of a cladogenetic split. ...
We use integrative taxonomy to elucidate species boundaries of the plant bug genus Pseudoloxops (Kirkaldy 1905) in the Austral and Society archipelagos of French Polynesia. We operationalize the unified species concept by treating each individual as a potential species and then establish initial groupings (putative species) following statistically highly-supported reciprocal monophyly of individuals in a phylogenetic analysis of CO1, 16S, and 28S gene fragments. We then test our species hypotheses against additional lines of evidence from geometric morphometrics, genetic distance, discrete genitalic morphology, plant association, and geographic distribution partitions. Twenty species endemic to French Polynesia are recognized as follows: Pseudoloxops aama Balukjian & Van Dam, sp. nov., Pseudoloxops anaana Balukjian & Van Dam, sp. nov., Pseudoloxops baileyi Balukjian & Van Dam, sp. nov., Pseudoloxops chastaoliancai Balukjian & Van Dam, sp. nov., Pseudoloxops harrisonfordi Balukjian & Van Dam, sp. nov., Pseudoloxops kamalaharrisae Balukjian & Van Dam, sp. nov., Pseudoloxops oboyskii Balukjian & Van Dam, sp. nov., Pseudoloxops papepihaa Balukjian & Van Dam, sp. nov., Pseudoloxops puarata Balukjian & Van Dam, sp. nov., Pseudoloxops raimana Balukjian & Van Dam, sp. nov., Pseudoloxops ravataputuarai Balukjian & Van Dam, sp. nov., Pseudoloxops simberloffi Balukjian & Van Dam, sp. nov., Pseudoloxops tairoto Balukjian & Van Dam, sp. nov., Pseudoloxops temehanirahi Balukjian & Van Dam, sp. nov., Pseudoloxops tiapai Balukjian & Van Dam, sp. nov., Pseudoloxops toparaamahana Balukjian & Van Dam, sp. nov., Pseudoloxops tupapaau Balukjian & Van Dam, sp. nov. New synonyms are proposed for Pseudoloxops flavus (Knight, 1937) [=Pseudoloxops rubrocuneatus (Knight, 1937)] and Pseudoloxops adamsoni (Knight, 1937) [= Pseudoloxops nigribasicornis (Knight, 1937) and = Pseudoloxops tahiticus (Knight, 1937)]. Pseudoloxops rubroclavus (Knight, 1937) is redescribed.
... Following the unified species concept (de Queiroz 1998(de Queiroz , 2007, we support the recognition of the species mentioned below based on morphological and phylogenetic criteria, which we interpret as evidence of lineage separation. ...
The taxonomic status of the skinks from Ecuador has never been carefully addressed. In this paper we examine populations of Mabuya lizards across Amazonian Ecuador in an attempt to establish their taxonomic identity and phylogenetic affinities. We confirm the presence of both M. altamazonica and M. nigropunctata and describe a new species from Yasuní National Park, one of the most biodiverse places on Earth. The new species differs from its congeners in lepidosis and color patterns. For the first time, we include samples from Ecuador in a molecular phylogenetic analysis of Mabuya , which confirms the monophyly of the new species and the taxonomic identity of both M. altamazonica and M. nigropunctata from Ecuador. The new species is closely related to M. bistriata . Finally, we present an identification key for species of Ecuadorian Mabuya .
... This may disqualify E. dolomiticus from being a subspecies of E. eugene-maraisii in the context of the Ecological Species Concept [123]. Moreover, the species may be legitimately delimited through the Unified Species Concept [124,125], which is similar to the Genealogical Species Concept [126], but whose only criterion is that populations are presently evolving independently from one another regardless of historical associations. This concept, therefore, acknowledges the possibility of species merging and separating through time, [127], which may have occurred in cycad species due to their ability to hybridise [86,89,94,128,129]. ...
Recent technological advancements in conservation genetics and genomics have resulted in diverse tools for aiding the conservation of species. The precision and resolution of high throughput sequencing technologies provide valuable insights to aid conservation decisions, but these technologies are often financially unfeasible or unavailable in resource constrained countries. Inter-Simple Sequence Repeat (ISSR) markers, when combined with sensitive automated detection systems, provide a simple, cheap means to investigate genetic diversity and discriminate closely related species. Here, we apply this technology to assess genetic diversity and taxonomic delimitation in the En-cephalartos eugene-maraisii species complex, a highly threatened, taxonomically dubious group of cycads in South Africa. Our analyses support the taxonomic singularity of E. dyerianus, E. dolomiticus and E. eugene-maraisii. Relationships between E. nubimontanus and E. cupidus remain uncertain. E. middelburgensis samples showed no clustering but had poor amplification success. This study demonstrates the suitability of automated ISSR fingerprinting as a method for plant conservation studies, especially in resource-constrained countries, and we make recommendations as to how this methodology can be effectively implemented.
... However, the first step in determining how many species (i.e. independently evolving metapopulation lineages) we have within this complex is selecting appropriate species recognition criteria from the nearly 30 existing examples (see de Queiroz, 1998de Queiroz, , 2007Sluys, 2021;Zachos, 2016;Zink, 1997). We adopted the GAGE species recognition criteria (Seifert, 2020) in the case of morphometric analyses because it relates to readily observable characteristics. ...
Temnothorax unifasciatus (Latreille, 1798) is a widely distributed pan-European species from the Iberian Peninsula to the Caucasus. This taxon's relatively high morphological variability prompts the taxonomists of earlier times and today to mention the morphologically different elements at specific or subspecific ranks. This paper aims to understand the population structure and genetic diversity within this lineage via integrative taxonomy, incorporating molecular phylo-genetics, species delimitation analyses and multivariate analyses of continuous morphometric data from across the geographic range of the T. unifasciatus complex. Phylogenetic analyses yielded incongruent trees. The genealogical diversity index (gdi) and the confirmatory analyses on morphological data found only weak, ambiguous delimitations within the unifasciatus complex. The most highly supported scenario splits T. brackoi from the remaining unifasciatus complex with ambiguous support (gdi = 0.56). This scenario is supported by multivariate morphometry with 100% accuracy in classification success. Instead, our results suggest complex morphological and genetic population structuring within the broad range of T. unifasciatus. Therefore, we confirm the validity of two species, T. brackoi Salata & Borowiec, 2019 and T. unifasciatus (Latreille, 1798), and propose
five new junior synonymies, T. cordieri (Bondroit, 1918) syn. nov., T. tauricus
(Ruzsky, 1902) syn. nov., T. berlandi (Bondroit, 1918) syn. nov., T. unifasciatus
staegeri (Bondroit, 1918) syn. nov., T. tuberum ciscaucasicus (Arnol'di, 1977) syn.
nov. with the latter. To achieve maximal taxonomic stability, we designated a
lectotype for Temnothorax unifasciatus (Latreille, 1798).
... Despite more than a century of effort, taxonomists have yet to reach a consensus on the concept of species and methods of all species delimitation (Mayden 1997;de Queiroz 1998;Fu and Zeng 2008;Yang and Rannala 2010;Chen et al. 2013;Peng et al. 2014). Trying to solve "the notorious problem of taxonomic uncertainty (Uetz et al. 2024)", Huang et al. (2021) proposed the principle of "species subdivision" with recommendable "subdivision" at the species level. ...
A new newt species, Hypselotriton huanggangensissp. nov., is described based on nine specimens collected from Huanggangshan Mountains, Yanshan County, Jiangxi, China. Morphologically, the new species is characterized by the combination of nine external characters: (1) obvious black patches with clear boundaries on the whole body; (2) ground color of the dorsal body tan; (3) ground color of venter bright orange; (4) skin rough; (5) vertebral ridge weak; (6) fingers and toes overlapping when forelimb and hindlimb adpressed towards each other along body; (7) postocular orange spot absent; (8) small white warty glands around the eye; (9) two discontinuous longitudinal lines formed by white warty glands from neck to lateral parts of tail. Molecularly, the new species forms an independent clade with strong support in the phylogenetic trees of the genus based on the mitochondrial locus of NADH dehydrogenase subunit 2 (ND2) gene fragments. The new species distinctly differs from H. fudingensis by differences in its body measurements, vertebral ridge, dorsal black patches, and ventral black patches. Furthermore, the new species and H. fudingensis are geographically isolated by a series of high mountain ranges, including the Wuyishan and Jiufengshan Mountains. The number of Hypselotriton species is now 11.
... Identifying species in the presence of gene flow is a contentious and difficult problem in systematic biology (Hillis et al. 2021). The general lineage species concept defines species as independently evolving metapopulation lineages (de Queiroz 1998). This requires that entities identified as species be on distinctive evolutionary trajectories, but does not preclude some gene flow occurring among them. ...
Gene flow between diverging lineages challenges the resolution of species boundaries and the understanding of evolutionary history in recent radiations. Here, we integrate phylogenetic and coalescent tools to resolve reticulate patterns of diversification and use a perspective focused on evolutionary mechanisms to distinguish interspecific and intraspecific taxonomic variation. We use this approach to resolve the systematics for one of the most intensively studied but difficult to understand groups of reptiles: the spotted whiptail lizards of the genus Aspidoscelis (A. gularis complex). Whiptails contain the largest number of unisexual species known within any vertebrate group and the spotted whiptail complex has played a key role in the generation of this diversity through hybrid speciation. Understanding lineage boundaries and the evolutionary history of divergence and reticulation within this group is therefore key to understanding the generation of unisexual diversity in whiptails. Despite this importance, long-standing confusion about their systematics has impeded understanding of which gonochoristic species have contributed to the formation of unisexual lineages. Using reduced representation genomic data, we resolve patterns of divergence and gene flow within the spotted whiptails and clarify patterns of hybrid speciation. We find evidence that biogeographically structured ecological and environmental variation has been important in morphological and genetic diversification, as well as the maintenance of species boundaries in this system. Our study elucidates how gene flow among lineages and the continuous nature of speciation can bias the practice of species delimitation and lead taxonomists operating under different frameworks to different conclusions (here we propose that a two species arrangement best reflects our current understanding). In doing so, this study provides conceptual and methodological insights into approaches to resolving diversification patterns and species boundaries in rapid radiations with complex histories, as well as long-standing taxonomic challenges in the field of systematic biology.
... De Queiroz [39] elaborated on how all species concepts are about two lineages somehow reproductively isolated while stressing the importance of such isolation in defining new species. While better sampling of contact zones and genomic data would be desirable, the difference between E. akayima sp. ...
While elucidating the evolutionary trajectory of green anacondas, we previously documented the existence of two distinct species, Eunectes akayima sp. nov. and Eunectes murinus (Linnaeus, 1758), that separated approximately 10 million years ago. Our research integrates a novel molecular clock approach, focuses on tectonic plate movements with fossil records as minimal chronological markers, and offers a refined understanding of speciation events in relation to major biogeographical occurrences in South America. Mitochondrial DNA analysis demonstrates a significant genetic divergence between the species, which is supported by a notable difference in sexual size dimorphism (SSD) intensity between the two species, along with other morphological differences. This paper also rectifies earlier oversights in the description of the new species and clarifies taxonomic ambiguities in compliance with the International Code of Zoological Nomenclature (henceforth ICZN). In addition, we designate a neotype for E. murinus to stabilize the group. In an effort to honor Indigenous nations, E. akayima sp. nov. derives its name from the Carib language, advocating for the inclusion of traditional names in scientific discourse. Our paper not only contributes to the taxonomic stability of anacondas but also advocates for the usage of Indigenous names in zoological nomenclature by adopting a more inclusive and flexible approach to the ICZN and eliminating unintended exclusionary practices that we have inherited in science as in other disciplines.
... This may disqualify E. dolomiticus from being a subspecies of E. eugene-maraisii in the context of the Ecological Species Concept [116]. Moreover, the species may be legitimately delimited through the Unified Species Concept [117,118], which is similar to the Genealogical Species Concept [119], but whose only criteria is that populations are presently evolving independently from one another regardless of historical associations. This concept therefore acknowledges the possibility of species merging and separating through time, [120] which may have occurred in cycad species given their ability to hybridise [76,79,84,121,122]. ...
Recent technological advancements in conservation genetics and genomics have resulted in diverse tools for aiding conservation of species. The precision and resolution of high throughput sequencing technologies provide valuable insights to aid conservation decisions, but these technologies are often financially unfeasible or unavailable in resource constrained countries. Inter-Simple Sequence Repeat (ISSR) markers, when combined with sensitive automated detection systems, provide a simple, cheap means to investigate genetic diversity and discriminate closely related species. Here we apply this technology to assess genetic diversity and taxonomic delimitation in the Encephalartos eugene-maraisii species complex, a highly threatened, taxonomically dubious group of cycads in South Africa. Our analyses support taxonomic singularity of E. dyerianus, E. dolomiticus and E. eugene-maraisii. Relationships between E. nubimontanus and E. cupidus remain uncertain. E. middelburgensis samples showed no clustering but had poor amplification success. This study demonstrates the suitability of automated ISSR fingerprinting as a method for plant conservation studies, especially in resource-constrained countries, and we make recommendations as to how this methodology can be effectively implemented.
... Indeed, within species that reproduce asexually, every individual is reproductively isolated from every other and thus on its own evolutionary path (Lin et al., 2017). Other criteria than interbreeding are thus necessary to demonstrate that a lineage evolves separately from others and with its own evolutionary tendencies (De Queiroz, 1998). This is the case for the earthworm species that reproduce by parthenogenesis and which are often polyploids (Briones et al., 2009); they are frequent in the Lumbricidae family and have also been reported in the Megascolecidae . ...
Specimen identification at the species level is a critical challenge for understanding community structure and conserving biodiversity. The use of mitochondrial DNA barcodes, in addition to morphology, has proven to be a useful tool for earthworm identification, but it has also raised difficulties. Thus, approaches to delineating molecular operational taxonomic units (MOTUs) from cytochrome c oxidase subunit 1 (COI) or 16S rDNA sequence data often reveal more mitochondrial lineages than morphospecies, raising the question of whether these MOTUs should be used as taxonomic entities in community structure studies. Here, we used a newly acquired dataset of 576 COI barcodes of earthworms from Metropolitan France that were clustered in 36 MOTUS, corresponding to 21 morphospecies. We also incorporated data gathered from the literature to investigate this question. In order to match our MOTUs with already-described mitochondrial lineages, we downloaded reference sequences from the GenBank and BOLD platforms. In light of the difficulties encountered in recovering these sequences, we recommend that any new mitochondrial lineage described in a study be named consistently with previous works. Next, we analyzed the biological, ecological, and molecular data available in the literature on the different mitochondrial lineages that matched our MOTUs in order to determine if there was a consensus for species delimitation. Although the study specimens mainly belong to the Lumbricidae, which is one of the most studied families of earthworms, the data are often missing to determine if the MOTUs correspond to different species. Pending revision of the taxonomy, MOTUs for which mitochondrial divergence has been confirmed by morphological differences should be considered distinct taxonomic entities in community structure studies. In the absence of morphological differences and pending more data, we propose to distinguish for these analyses, within sexually reproducing morphospecies, the MOTUs for which mitochondrial divergence has been confirmed by multilocus nuclear data, while in the case of reproduction by parthenogenesis, ecological differences between MOTUs are necessary to consider them as different taxonomic entities.
... We assume that species represent 'metapopulational lineage segments' (see de Queiroz, 1998de Queiroz, , 2005 and that different sources of information (e.g., morphological, molecular data) are potentially informative in species delimitation. Thus, the different species of Characidium occurring in the analysed ecoregions were delimited considering all available specimens through the application of analyses based on molecular and morphological data as presented above. ...
Characidium represents the most widely distributed and species-rich fish genus within the family Crenuchidae in the Neotropical region, with numerous species described over the last decade. Despite this taxonomic progress, the understanding of species boundaries and population variation within the genus remains limited. In response, an integrative study was undertaken, utilizing both morphological and molecular data from neotropical freshwater ecoregions with rivers that drain the Brazilian northeastern. The primary objective of this investigation was to elucidate taxonomic delimitations and, where relevant, propose new species hypotheses. Our results propose the existence of 15 operational taxonomic units (OTUs) as species hypotheses. Among these, 10 were identified as valid species, four represented morphotypes that hold the potential of constituting new species, and one OTU was determined as a new species, corroborated by all proposed delimitation methods. Our results demonstrated discrepancies between morphological and molecular data, highlighting the challenges in defining taxonomic boundaries within Characidium. Moreover, our findings provided insights into the intricate diversification history of Characidium species, applied to the species that occur in northeastern Brazilian drainages. We proposed that historical events, such as river connections and barriers, have played a significant role in shaping the current distribution patterns of the genus.
... Groves' ( , 2012Groves' ( , 2014 cogently defended his use of the PSC, defined by Cracraft (1983) as "an irreducible cluster of organisms that is diagnosably distinct from other such clusters, and within which there is a parental pattern of ancestry and descent." It is essentially an evolutionary notion of the species as was argued by Simpson (1951). De Queiroz (1998 proposed a general lineage concept of species that reconciled many of the numerous species concepts (see Mallet, 2001) as just being different methods to delimit species. De Queiroz (2007) emphasized that "One of the most important consequences of a unified species concept is that it clarifies the issue of species delimitation by clearl ...
The database of the IUCN SSC Primate Specialist Group currently (December
2023) registers 218 species and subspecies of Neotropical primates in 24 genera
and five families. In the early 1960s, the diversity of Neotropical primates was
estimated to be around 200 species and subspecies. From then, through the
1970s to the mid-1990s, however, the perception of the region’s primate
diversity dropped, and reached an all-time low at 83 species and subspecies in
1980 (A World List of Mammalian Species, G. B. Corbet and J. E. Hill, British
Museum (Natural History), Comstock Publishing, Cornell University Press,
London and Ithaca). Interest in taxonomy and primate field research in the
Neotropics was subdued up to the late 1970s. Change was sparked by the
burgeoning capture of primates for biomedical research in the 1950s and 1960s,
and the increasing destruction of the Amazon rainforests from the late 1970s.
The numbers increased, at first slowly, but then, in 1995, they leapt back to the
200s in anticipation of a book by C. P. Groves (2001, Primate Taxonomy,
Smithsonian Institution Press, Washington, DC). The species’ counts (not
including subspecies) rose due to the adoption of the Phylogenetic Species
Concept over the Biological Species Concept, the former favoring the category
of species over subspecies. In this article, we discuss the changes in species and
subspecies numbers in the classification of the Neotropical primates, and report
on the taxonomic changes resulting from taxonomic research ongoing since
2012. We emphasize the importance of taxonomic research for an understanding
of the diversity of primates, and for conservation planning, not least in identifying
the populations that are threatened.
... They are gene trees, intended to be a first species partition hypothesis on which further work should be carried out (Puillandre et al. 2012, Zhang et al. 2013, and thus they are useful to analyse diversification processes. These analyses, the phylogenetic support of nodes, and the genetic distance analyses allow delineation of monophyletic groups or clades (units consisting of an ancestral species and its descendants, de Queiroz 1998de Queiroz , 2007 with no taxonomic standing until more lines of evidence are examined. ...
Phenotypic clines reflect variation in niche-related phenotypic attributes across species' ranges, which may arise from ecological speciation along environmental gradients. Clinal variation without divergence is also possible if the fundamental niche is broad and no significant barriers to dispersal exist. The Peromyscus difficilis species group occurs in North American highlands, showing clinal morphometric variation interpreted as evidence of continuous gene flow. Yet, recent molecular analyses have documented phylogenetic structure. We examined phylogeny, morphological phylogenetic signal (MPS), and phylogenetic niche conservatism (PNC) to investigate the processes resulting in the cline. Morphometric and niche attributes were strongly correlated. Genetic diversification was found, starting in the late Miocene from ancestral populations with a broad fundamental niche, which allowed dispersion across temperate North America. North-to-south Pliocene aridification isolated the northernmost populations in mountain islands, promoting diversification and creating a PNC pattern for the northern populations. For Central Mexico MPS and PNC were detected for a few populations that are diversifying in some areas, with no apparent niche shifts. We propose that clinal variation has resulted from broad environmental tolerances allowing dispersal, with size responding to local conditions, whereas phylogenetic structure is mostly the result of historical isolating events that do not necessarily reflect phenotypic or niche-related variation.
... The taxonomic conclusions of this study are based on the observation of morphological features and color patterns, as well as on previously inferred phylogenetic relationships based on molecular data (Páez & Ron 2019). We consider this information to fulfill the species delimitation criteria following a general lineage or unified species concept (de Queiroz 1998(de Queiroz , 2007. ...
Based on morphological and previously published molecular evidence, herein we describe two new
species of Pristimantis from the Andes of northern Peru; Pristimantis sp. nov. 1 from Cañaris in the northern
region of the Cordillera Occidental of the Andes, at an elevation of 3200 m.a.s.l., Lambayeque Department,
northwestern Peru, and Pristimantis sp. nov. 2 from the Huarmicocha to Cochabamba trail in the northern region
of the Cordillera Central, at an elevation of 3376 m.a.s.l., Amazonas Department, northeastern Peru. Both new
species are morphologically similar to and were previously confused with Pristimantis phoxocephalus, because
they shared (i) the presence of a pointed rostral papilla, (ii) acutely or acuminated shaped snout in dorsal view,
and (iii) in life, distinctive coloration on groin and concealed surfaces of thighs. However, the new species are not
closely related to species from the P. phoxocephalus group and can be readily diagnosed from morphologically
similar Pristimantis from Peru and Ecuador by the combination of the following characters: snout shape,
tuberculate or coarsely tuberculate dorsum, and the color of concealed surfaces of thighs and groin.
... As in previous studies, we follow the general lineage concept (de Queiroz 1998(de Queiroz , 2007 in combination with a relaxed biological species criterion, i. e., demanding reproductive isolation indicated by restricted gene flow among lineages (e. g., Speybroeck et al. 2020). Because reproductive barriers generated through time increase genealogical depth and agreement among unlinked loci (Avise & Wollenberg 1997), we use genealogical concordance (Avise & Ball 1990) between mitochondrial and nuclear loci, especially in populations occurring in sympatry or close geographical proximity, as an indicator for restricted gene flow. ...
The Gephyromantis moseri complex, classified in the mantellid subgenus Duboimantis, currently contains one species of frog, G. moseri (Glaw & Vences, 2002) from the Andasibe area in the Northern Central East of Madagascar, as well as several genetically divergent populations from the North East that have been provisionally assigned to the species. We here analyse DNA sequences of one mitochondrial (16S rRNA) and one nuclear-encoded gene (RAG-1), morphology, and advertisement calls of newly collected material of this species complex from various localities in Madagascar. Based on this integrative evidence, in particular concordant nuclear gene differentiation between seven highly divergent (> 4 %) mitochondrial lineages, as well as differences in advertisement call structure, body size and head shape between some of these lineages, we conclude that the G. moseri complex contains several additional species of which four are formally named and described in this study: G. fuscus sp. nov., a rather small-sized species sister to G. moseri, occurring in two sites (Mahasoa and the western part of the Makira Reserve), G. makira sp. nov., a species known from only one available voucher specimen from eastern Makira, G. bemiray sp. nov. from eastern Makira, Masoala, and Ambolokopatrika; and G. ampondo sp. nov. from Marojejy in the North East. Two further lineages for which voucher specimens were not available in the framework of this study are considered unconfirmed candidate species G. sp. Ca19 and G. sp. Ca33, pending the collection of further material. The revision of the G. moseri complex adds to the diversity of Duboimantis and once more demonstrates the existence of secretive or genuinely rare restricted-range species among the Malagasy frogs whose inventory can only be completed by further fieldwork and integrative taxonomic research.
... Over the last decades, it has taken advantage of the rapid advances in molecular biology and bioinformatics in order to infer more objectively and more rapidly robust and testable species hypotheses. This approach relies on the interpretation of species as independent evolutionary lineages [5,6] and is in line with the paradigm of integrative taxonomy, according to which various lines of evidence and a wide range of data types can be used in formalized analytical workflows to propose species Among the many characters that can be applied to propose species hypotheses, DNA barcodes are often readily accessible and can be easily formalized for analysis as a single-locus sequence alignment, often of uniparental inheritance such as mitochondrial DNA (1, 9; see also Chap. 4 by Miralles et al.). Different algorithms have been specifically proposed to produce species partitions from such single locus alignments. ...
DNA barcoding plays an important role in exploring undescribed biodiversity and is increasingly used to delimit lineages at the species level (see Chap. 4 by Miralles et al.). Although several approaches and programs have been developed to perform species delimitation from datasets of single-locus DNA sequences, such as DNA barcodes, most of these were not initially provided as user-friendly GUI-driven executables. In spite of their differences, most of these tools share the same goal, i.e., inferring de novo a partition of subsets, potentially each representing a distinct species. More recently, a proposed common exchange format for the resulting species partitions (SPART) has been implemented by several of these tools, paving the way toward developing an interoperable digital environment entirely dedicated to integrative and comparative species delimitation. In this chapter, we provide detailed protocols for the use of two bioinformatic tools, one for single locus molecular species delimitation (ASAP) and one for statistical comparison of species partitions resulting from any kind of species delimitation analyses (LIMES).
... This may disqualify E. dolomiticus from being a subspecies of E. eugene-maraisii in the context of the ecological species concept [112]. Moreover, the species may be legitimately delimited through the Unified Species Concept [113,114], which is similar to the Genealogical Species Concept [115], but whose only criteria is that populations are presently evolving independently from one another regardless of historical associations. This concept therefore acknowledges the possibility of species merging and separating through time, [116] which may have occurred in cycad species given their ability to hybridise [76,79,84,117,118]. ...
Recent technological advancements in conservation genetics and genomics have resulted in diverse tools for aiding conservation of species. The precision and resolution of high throughput sequencing technologies provide valuable insights to aid conservation decisions, but these technologies are often financially unfeasible or unavailable in resource constrained countries. Inter-Simple Sequence Repeat (ISSR) markers, when combined with sensitive automated detection systems, provide a simple, cheap means to investigate genetic diversity and discriminate closely related species. Here we apply this technology to assess genetic diversity and taxonomic delimitation in the Encephalartos eugene-maraisii species complex, a highly threatened, taxonomically dubious group of cycads in South Africa. Silica dried cycad leaflets were extracted using the Oktopure robot employing Sbeadex chemistry and amplified with fluorescently tagged ISSR primers. Band presence was scored with an ABI 3130 genetic sequencer under three different fluorescence cut-off values. Phenetic analyses were performed in NTSYS software while Bayesian analysis was performed in STRUCTURE, and haplotype network analysis, AMOVA and Tajima’s D statistic was computed with PopART. Our analyses support taxonomic singularity of E. dyerianus, E. dolomiticus and E. eugene-maraisii. Relationships between E. nubimontanus and E. cupidus remain uncertain. E. middelburgensis samples showed no clustering but had poor amplification success. This study demonstrated the suitability of automated ISSR fingerprinting as a method for plant conservation studies, especially in resource-constrained countries.
This chapter not only explains the taxonomic concept applied in this book, but also introduces the reader into the general debate about species concepts, arising from their use for different purposes with taxonomy serving as a basic tool. Conceptually species determination starts with an individual. Several individuals that share enough characters can be grouped into ‘species’, distinct from other ‘species’. A description of those distinguishing characters should allow for indisputable identification. Whereas “species” is generally accepted as the basic entity for describing the overwhelming diversity to which life has evolved, there is still an ongoing debate in biology about “species concepts”. When this monograph was being prepared there were lively debates about “species” delineation. All of the arguments discussed turned out to be non-decisive by themselves—in fact, in each case scientists resolved on agreed concepts for species, instead of being completely objective. This illustrated once again that not only “species are hypotheses” but, moreover, species are man-made agreements, based on a certain concept which needs (A) to be defined accurately and (B) which has been developed with a well-articulated objective.
The conservation and management of coral reef ecosystems will benefit from accurate assessments of reef-building coral species diversity. However, the true diversity of corals may be obfuscated by cryptic yet genetically distinct groups, which are likely more pervasive than currently recognised. Here, we investigate the prevalence of cryptic coral groups and assess evidence for their permeability to gene flow (hybridisation) via a structured literature review of genomic studies. Using reproducible criteria to detect distinct genetic groups that are sympatric, we find that 68% of nominal species represented in population genomic studies show evidence for comprising partially reproductively isolated groups and that these distinct groups are often linked by gene flow. Cryptic genetic groups frequently segregate by environment, especially depth, and may differ by phenotypic characteristics including resilience to heat stress. This hidden biodiversity creates challenges for coral conservation and restoration planning that are not well appreciated, including hiding true population declines, biasing estimates for species’ phenotypic breadth, overestimating the resilience of species to stressors, yielding uncertainty in evolutionary dynamics inferred from past studies, and implying that reproductive barriers may limit mating between local and translocated corals. Incorporating the expectation that coral cryptic taxa with incomplete species boundaries will frequently be encountered is critical to the long-term success of coral conservation and restoration programs. Studying these phenomena in more detail will directly benefit conservation and restoration goals. Thus, we detail recommendations for best practice and strategies for identifying cryptic taxa and hybridisation. In addition, cryptic coral taxa present an untapped resource for studying speciation which could provide rich opportunities for collaboration among coral and speciation biologists and fill key knowledge gaps relevant to conservation and restoration.
A new species of rock skink Liopholis Fitzinger 1843 (Scincidae) is described from the Mann-Musgrave ranges of northwestern South Australia. Liopholis margaretae sensu lato (Storr 1968) is currently known to occur in two disjunct populations: the MacDonnell ranges bioregion and nearby regions in the Northern territory, and the Central ranges bioregion in South Australia. Based on morphological examination of both museum and field specimens, as well as on newly generated molecular data, we show that specimens from these two ranges constitute distinct species. the new species, Liopholis aputja sp. nov. is endemic to a specific geological landform (Mann-Musgrave ranges) within the Central ranges bioregion, and is estimated to have diverged from the MacDonnell ranges population during widespread aridification of the Miocene. Liopholis aputja sp. nov. is distinguished from congeners by a combination of its moderately large size (SVL up to 135 mm), relatively pointed snout, smooth dorsal scales, black and calloused subdigital lamellae and soles of feet, and possessing usually six supraciliary scales and usually four enlarged ear lobules. this new species adds to the list of endemic herpetofauna recognised in the Central ranges bioregion.
Ctenomys (tuco-tucos) is one of the most speciose genera of mammals, with around 70 described species. Recently, the rate of new species descriptions within the genus Ctenomys has notably increased, primarily due to recent taxonomic revisions and surveys in previously unexplored geographic areas. In this study, utilizing both morphological and molecular evidence, we describe a new species of Ctenomys from northern Argentine Patagonia, confined between the Colorado and Negro rivers. This new species is a member of the Magellanicus group displaying close relationships with other species distributed in northern Patagonia and adjacent regions (C. bidaui, C. miguelchristie, C. pontifex, and C. pulcer). The major rivers in the region (Colorado and Negro rivers) appear to delineate the distributional boundaries of the identified taxa. We therefore propose that rivers, acting as natural barriers to dispersal, have significantly influenced the diversity of Ctenomys in northern extra-Andean Patagonia.
The Malagasy stream-breeding treefrog species Boophis marojezensis contains bioacoustically and genetically highly divergent populations. Some of these populations have been defined as candidate species and emit somewhat bizarre advertisement calls consisting of multiple whistle-notes. We here enable a long-overdue taxonomic revision of this species complex by applying a museomics approach to sequence DNA from the holotype of B. marojezensis . Based on an integrative approach that combines divergence levels in mitochondrial DNA and in three nuclear-encoded genes, morphological data, and bioacoustic comparisons, we conclude that eight different species exist in this complex, seven of which are formally described herein as new. Although morphological differences between species are small and mainly separate small-sized from larger-sized species, conclusive evidence for the new species comes from their sympatric and sometimes syntopic occurrence without haplotype sharing in three nuclear genes and under maintenance of bioacoustic differences. Uncorrected genetic divergences in the mitochondrial 16S rRNA gene are >3% in almost all cases, and in some cases up to 8%. In reference to the otherworldly sounds by which these frogs fill Malagasy rainforests, some of them reminiscent of sounds of technical equipment in the fictional “Star Trek” universe, we here name and describe the seven new species in honor of fictional captains of starships, namely B. kirki sp. nov. , B. picardi sp. nov. , B. siskoi sp. nov. , B. janewayae sp. nov. , B. archeri sp. nov. , B. pikei sp. nov. , and B. burnhamae sp. nov. The majority of these species occur in northern Madagascar, where up to three species can occur in immediate geographical proximity, e.g., B. marojezensis , B. burnhamae sp. nov. and B. pikei sp. nov. at different elevations in the Marojejy Massif. South of 16°S latitude, only B. janewayae sp. nov. , B. picardi sp. nov. , and B. kirki sp. nov. are found, with the latter extending southwards to Ranomafana National Park. Our study confirms the existence of numerous morphologically cryptic and microendemic species among Madagascar’s amphibians, some of which are known only from unprotected sites and require adequate conservation management.
Salamanders of the genus Lyciasalamandra are represented by as many as 20 narrow-range endemic taxa inhabiting the Mediterranean coast of Turkey and a handful of Aegean Islands. Despite recent molecular phylogenetic studies, the genus is rife with uncertainty about the number of contained species and their phylogenetic relationships, both of which can interfere with needed conservation actions. To test species limits and infer interrelationships we generated as many as 113,176 RAD loci containing 229,427 single nucleotide polymorphisms (SNPs), for 110 specimens of Lyciasalamandra representing 19 of the 20 described taxa. Through a conservative species delimitation approach, we found support for eight species in the genus which broadly agree with currently described species-level diversity. We then use multiple coalescent-based species tree methods to resolve relationships in this relatively old, synchronous species radiation. We recommend synonymization of the largely over-split subspecific taxa, and the elevation of L. luschani finikensis to full species status as L. finikensis. Our hope is that this revised taxonomic framework provides a stable foundation for conservation management in these fragile, microendemic taxa.
Speciation is the original source of all species richness. Here, I address two questions: (1) what might typical speciation look like across life? and (2) how has speciation led to the diversity of life we see today? What is "typical" depends on the richness of different groups. In groups associated with host organisms (which may dominate numerically), the processes of co-speciation and host switching are crucial. Among free-living organisms, allopatric speciation, ecological divergence, and prezygotic isolation appear widely important. Yet, the processes by which species become allopatric (and initially split) remain highly unclear. Among macroscopic organisms, the processes underlying the speciation of cryptic insect lineages may predominate, and are briefly reviewed here. Analyses of diversification rates among clades can illuminate the factors that drive speciation and species richness, and I review the advantages and disadvantages, of different methods for estimating diversification rates. Patterns of species richness among named clades are generally related to variation in diversification rates, and specific types of ecological variables seem to underlie variation in diversification rates at different scales. Nevertheless, many richness patterns are unrelated to diversification rates and may be related to the time available for speciation instead, including richness among regions, clades, and traits.
Within the genus Cacosternum, the species C. capense and C. namaquense form a clade defined by their robust morphology, large size, and distinct dorsolateral glands. In this study, we describe a third member of the group endemic to the Cederberg region of South Africa. Specimens from this area have historically been assigned to C. karooicum, but here we show that this population is genetically unrelated. Using a combination of molecular, morphological, and acoustic data, we provide evidence to show that the Cederberg population of C. karooicum represents
n undescribed species within the C. capense group. The new species can be diagnosed from its closest phylogenetic relatives, C. capense and C. namaquense, by the absence of a dark streak running downwards from the pupil into the iris, the presence of large rictal glands that form an uninterrupted arc with the angle of the jaw, heart-shaped palmar tubercles, and an advertisement call with a dominant frequency below 2 kHz. We further discuss their natural history, distribution, and conservation.
Four species of the genus Panaspis-P. cabindae, P. wahlbergii, P. maculicollis and P. mocamedensis-are currently known from Angola. The analysis of recently collected specimens from Serra da Neve Inselberg, an isolated mountain located in northern Na-mibe Province, revealed unexpected taxonomic diversity in the group. Using an integrative taxonomy approach based on morphological and DNA sequence data, with both mitochondrial (16S) and nuclear (RAG-1) genes, we were able to distinguish two distinct populations, described here as two new species, Panaspis ericae sp. nov. and P. mundavambo sp. nov. Both species are assumed to be endemic to the inselberg. This reinforces our notion of southwestern Angola as a hotspot of skink diversity, and highlights the urgent need for the conservation of Serra da Neve.
A new species of Heuchera (Saxifragaceae) from western North Carolina is described and illustrated herein, including phylogenomic and morphological analyses of its closest allies in the Heuchera parviflora group. Heuchera tuckasegeensis is distinguished from the other Heuchera taxa based on its distinct morphological attributes (style and stamen length, petiole and laminar hair length, and degree of leaf lobing), phylogenetic position, habitat preferences, and edaphic substrate specialization.
The Montseny brook newt (Calotriton arnoldi), a glacial relict endemic to a small,
isolated massif in northeast Spain, is considered the only Critically Endangered
urodele in Europe. Its restricted range is divided by a deep valley that acts as an
impassable barrier to dispersal, separating two isolated metapopulations (Western
and Eastern) that correspond to independent lineages with different evolutionary
trajectories, based on genetic and genomic data. Here, we address the ecological
differentiation between lineages and discuss its potential effect on the phenotypic
distinctness of each lineage. Based on multiple lines of evidence, we formally describe the Western Montseny brook newt as a new subspecies: Calotriton arnoldi laietanus ssp. nov. Finally, our study underscores the importance of considering taxonomic progress in the conservation policies of endangered species, ensuring appropriate management and protection of the newly described taxa.
The Lygodactylus tolampyae complex includes several deep genetic lineages of small diurnal geckos from the West and North West of Madagascar whose taxonomy is largely unsolved. We sequenced DNA fragments of one mitochondrial and four nuclear-encoded genes for up to 70 samples across the entire known range of these geckos. We find as many as 11 mitochondrial lineages differentiated by >4% pairwise distances in the 16S rRNA gene fragment, with >9% pairwise distance for the majority of lineage comparisons. Many of these lineages were concordantly differentiated in all of the nuclear-encoded genes without any haplotype sharing, despite the syntopic occurrence of some of them. We therefore hypothesize that the complex contains seven candidate species, but a comprehensive taxonomic resolution is complicated by various hindrances. These include incomplete sampling, with two lineages each known only from a single specimen, and one further lineage with no voucher specimens available for examination. Further hurdles are the probably lost holotype of L. tolampyae and its imprecise type locality, as well as the apparent lack of any morphological differentiation between the majority of the genetic lineages. Based on a survey of historical literature and the travel routes of the original collector, A. Grandidier, we conclude that the provenance of the holotype of L. tolampyae is likely in the wider Morondava area in the West and assign the sole candidate species from this area to this name. We then proceed to describe three species that represent separate genetic lineages for all markers studied: Lygodactylus morii sp. nov., a species common in Ankarafantsika National Park and several nearby sites in the North West; L. herilalai sp. nov., a species occurring in close syntopy with L. morii in Ankarafantsika without any signal of genetic admixture; and L. schwitzeri sp. nov. from Sahamalaza Peninsula in the North West. This leaves three more lineages without a name and with the need to gather additional samples, two from Namoroka National Park and one from other sites in the North West. We confirm the L. tolampyae complex to be an apparently rare example of truly cryptic reptile species in Madagascar, where even detailed morphological examination does not reveal morphological differences among lineages that are clearly evolutionarily independent and require recognition as distinct species due to their co-occurrence without admixture.
In biology, theories are constantly enriched and adapted by new examples and scientific advances. In this chapter, we focus on the debate about the rules in biology and their persistence over time as rules accepted by the scientific community. We exemplify this with Darwin’s theory of natural selection, which has been nourished by new disciplines and technologies during the twentieth and twenty-first centuries and has undergone transformations, although it undoubtedly remains the dominant explanation of the evolution of biological systems. Biological rules are dynamic, although they tend to remain relatively stable over time, and their response to the appearance of exceptions can be variable, although the integration of new knowledge into the field is usually gradual until the accumulation of exceptions is so significant that the applicability of the rules is questioned (crisis sensu Kuhnian revolution of scientific knowledge). We illustrate this concept by analyzing the historical evolution of biological species concepts, and we draw attention to the extrapolation of rules originally proposed for certain organisms and applied indiscriminately to other groups without exhaustive testing (e.g., eco-geographic rules).
Kinosternon is the most speciose genus of extant turtles, with 22 currently recognized species, distributed across large parts of the Americas. Most species have small distributions, but K. leucostomum and K. scorpioides range from Mexico to South America. Previous studies have found discordance between mitochondrial and nuclear phylogenies in some kinosternid groups, with the current taxonomy following the nuclear-based results. Herein, based on extended molecular, geographic, and taxonomic sampling, we explore the phylogeographic structure and taxonomic limits for K. leucostomum and the K. scorpioides group and present a fossil-calibrated nuclear time tree for Kinosternon. Our results reveal contrasting differentiation patterns for the K. scorpioides group and K. leucostomum, despite overlapping distributions. Kinosternon leucostomum shows only shallow geographic divergence, whereas the K. scorpioides group is polyphyletic with up to 10 distinct taxa, some of them undescribed. We support the elevation of K. s. albogulare and K. s. cruentatum to species level. Given the deep divergence within the genus Kinosternon, we propose the recognition of three subgenera, Kinosternon, Cryptochelys and Thyrosternum, and the abandonment of the group-based classification, at least for the K. leucostomum and K. scorpioides groups. Our results show an initial split in Kinosternon that gave rise to two main radiations, one Nearctic and one mainly Neotropical. Most speciation events in Kinosternon occurred during the Quaternary and we hypothesize that they were mediated by both climatic and geological events. Additionally, our data imply that at least three South American colonizations occurred, two in the K. leucostomum group, and one in the K. scorpioides group. Additionally, we hypothesize that discordance between mitochondrial and nuclear phylogenetic signal is due to mitochondrial capture from an extinct kinosternine lineage.
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