scholarly journals An overview of speciation and species limits in birds

The Auk ◽  
2021 ◽  
Author(s):  
Kevin Winker
Keyword(s):  
Gene Flow ◽  
Integrative Taxonomy ◽  
Difficult Problem ◽  
Biological Species ◽  
Biological Species Concept ◽  
Species Limits ◽  
Main Driver ◽  
Data Signal ◽  
Clear Line ◽  
Silver Bullet

Abstract Accurately determining avian species limits has been a challenge and a work in progress for most of a century. It is a fascinating but difficult problem. Under the biological species concept, only lineages that remain essentially independent when they are in sympatry are clearly species. Otherwise, there is no clear line yet found that marks when a pair of diverging lineages (e.g., in allopatry) become different enough to warrant full biological species status. Also, with more data, species limits often require reevaluation. The process of divergence and speciation is itself very complex and is the focus of intense research. Translating what we understand of that process into taxonomic names can be challenging. A series of issues are important. Single-locus criteria are unlikely to be convincing. Genetic independence is not a species limits requirement, but the degree of independence (gene flow) needs to be considered when there is opportunity for gene flow and independence is not complete. Time-based species (limits determined by time of separation) are unsatisfactory, though integrating time more effectively into our datasets is warranted. We need to disentangle data signal due to neutral processes vs. selection and prioritize the latter as the main driver of speciation. Assortative mating is also not likely to be an adequate criterion for determining species limits. Hybridization and gene flow are more important than ever, and there is a condition not being treated evenly in taxonomy: evolutionary trysts of 2 or more lineages stuck together through gene flow just short of speciation over long periods. Comparative methods that use what occurs between good species in contact to infer species limits among allopatric forms remain the gold standard, but they can be inaccurate and controversial. Species-level taxonomy in birds is likely to remain unsettled for some time. While the study of avian speciation has never been more exciting and dynamic, there is no silver bullet for species delimitation, nor is it likely that there will ever be one. Careful work using integrative taxonomy in a comparative framework is the most promising way forward.

scholarly journals Untangling systematics of the Paramacrobiotus areolatus species complex by an integrative redescription of the nominal species for the group, with multilocus phylogeny and species delineation in the genus Paramacrobiotus

2020 ◽  
Vol 188 (3) ◽  
pp. 694-716 ◽  
Author(s):  
Daniel Stec ◽  
Łukasz Krzywański ◽  
Krzysztof Zawierucha ◽  
Łukasz Michalczyk
Keyword(s):  
Dna Sequences ◽  
Integrative Taxonomy ◽  
Genetic Distances ◽  
Biological Species ◽  
Biological Species Concept ◽  
Nominal Species ◽  
Species Delineation ◽  
F1 Hybrid ◽  
Complex Species ◽  
History Of

Abstract Incomplete descriptions of nominal taxa are one of the most significant obstacles in modern taxonomy, including the taxonomy of Tardigrada. Another major problem in tardigrade systematics is the lack of tests for the reliability of genetic markers in species delineation. Here, we employ an integrative taxonomy approach to redescribe the nominal taxon for the P. areolatus complex, Paramacrobiotus areolatus. Moreover, we obtained multilocus DNA sequences for another 16 populations representing 9–12 Paramacrobiotus species collected from Europe, North America, Africa and Australia, enabling us to reconstruct the most extensive phylogeny of the genus to date. The identification of a pair of potentially cryptic dioecious P. areolatus complex species with divergent genetic distances in ITS2 (1.4%) and COI (13.8%) provided an opportunity to test the biological species concept for the first time in the history of tardigrade taxonomy. Intra- and interpopulation crosses did not differ in reproductive success in terms of F1 offspring. However, because of the low F1 family sizes, we were unfortunately unable to test F1 hybrid fertility. Although our results are only partially conclusive, they offer a baseline not only for further taxonomic and phylogenetic research on the areolatus complex, but also for studies on species delineation in tardigrades in general.

Species limits and taxonomy in birds

The Auk ◽  
2021 ◽  
Author(s):  
Kevin Winker ◽  
Pamela C Rasmussen
Keyword(s):  
Case Studies ◽  
Species Delimitation ◽  
Population Genomics ◽  
Species Concept ◽  
Biological Species ◽  
Integrative Approach ◽  
Population Divergence ◽  
Biological Species Concept ◽  
Species Limits ◽  
American Kestrel

Abstract Despite the acknowledged importance of defining avian species limits to scientific research, conservation, and management, in practice, they often remain contentious. This is true even among practitioners of a single species concept and is inevitable owing to the continuous nature of the speciation process, our incomplete and changing understanding of individual cases, and differing interpretations of available data. This issue of Ornithology brings together several papers on species limits, some more theoretical and general, and others case studies of specific taxa. These are viewed primarily through the lens of the biological species concept (BSC), by far the most widely adopted species concept in influential ornithological works. The more conceptual contributions focus on the importance of the integrative approach in species delimitation; the importance of considering selection with the increasing use of genomic data; examinations of the effectiveness of the Tobias et al. character-scoring species limits criteria; a review of thorny issues in species delimitation using examples from Australo-Papuan birds; and a review of the process of speciation that addresses how population divergence poses challenges. Case studies include population genomics of the American Kestrel (Falco sparverius); an integrative taxonomic analysis of Graceful Prinia (Prinia gracilis) that suggests two species are involved; and a reevaluation of species limits in Caribbean Sharp-shinned Hawk (Accipiter striatus) taxa.

Species limits in Antbirds (Aves: Passeriformes: Thamnophilidae): an evaluation of Plumbeous Antvireo (Dysithamnus plumbeus) based on vocalizations

Zootaxa ◽  
2008 ◽  
Vol 1726 (1) ◽  
pp. 60 ◽  
Author(s):  
MORTON L. ISLER ◽  
PHYLLIS R. ISLER ◽  
BRET M. WHITNEY
Keyword(s):  
20Th Century ◽  
Species Concept ◽  
Biological Species ◽  
Southeastern Brazil ◽  
Biological Species Concept ◽  
Species Status ◽  
Species Limits ◽  
The Andes ◽  
Northern Peru ◽  
Contrary Evidence

Through most of the 20th Century, Dysithamnus plumbeus was considered to comprise three geographically remote subspecies based on plumage: D. p. plumbeus of the lowlands of southeastern Brazil; D. p. leucostictus of the east slope of the Andes from central Colombia to extreme northern Peru; and D .p tucuyensis endemic to the mountains of northern Venezuela. Some recent authors have elevated these taxa to species status without providing additional evidence. We analyzed vocal differences among these taxa and compared the extent of diagnostic differences to a benchmark for species status under the Biological Species Concept (BSC). Vocalizations of D. plumbeus differed sufficiently from the others for D. plumbeus to be considered specifically distinct. Although both calls and loudsongs of the two remaining taxa differed from each other in some aspects, the differences did not meet our benchmark for species separation. We therefore recommend that they be designated as D. leucostictus leucostictus and D. leucostictus tucuyensis pending the acquisition of additional vocal recordings or other contrary evidence.

scholarly journals Endosperm-based hybridization barriers explain the pattern of gene flow between Arabidopsis lyrata and Arabidopsis arenosa in Central Europe

2017 ◽  
Vol 114 (6) ◽  
pp. E1027-E1035 ◽  
Author(s):  
Clément Lafon-Placette ◽  
Ida M. Johannessen ◽  
Karina S. Hornslien ◽  
Mohammad F. Ali ◽  
Katrine N. Bjerkan ◽  
...  
Keyword(s):  
Gene Flow ◽  
Central Europe ◽  
Diploid Species ◽  
Biological Species ◽  
Biological Species Concept ◽  
Interspecific Gene Flow ◽  
Seed Formation ◽  
Arabidopsis Lyrata ◽  
Hybrid Seeds ◽  
Arabidopsis Arenosa

Based on the biological species concept, two species are considered distinct if reproductive barriers prevent gene flow between them. In Central Europe, the diploid species Arabidopsis lyrata and Arabidopsis arenosa are genetically isolated, thus fitting this concept as “good species.” Nonetheless, interspecific gene flow involving their tetraploid forms has been described. The reasons for this ploidy-dependent reproductive isolation remain unknown. Here, we show that hybridization between diploid A. lyrata and A. arenosa causes mainly inviable seed formation, revealing a strong postzygotic reproductive barrier separating these two species. Although viability of hybrid seeds was impaired in both directions of hybridization, the cause for seed arrest differed. Hybridization of A. lyrata seed parents with A. arenosa pollen donors resulted in failure of endosperm cellularization, whereas the endosperm of reciprocal hybrids cellularized precociously. Endosperm cellularization failure in both hybridization directions is likely causal for the embryo arrest. Importantly, natural tetraploid A. lyrata was able to form viable hybrid seeds with diploid and tetraploid A. arenosa, associated with the reestablishment of normal endosperm cellularization. Conversely, the defects of hybrid seeds between tetraploid A. arenosa and diploid A. lyrata were aggravated. According to these results, we hypothesize that a tetraploidization event in A. lyrata allowed the production of viable hybrid seeds with A. arenosa, enabling gene flow between the two species.

scholarly journals Genes and speciation: is it time to abandon the biological species concept?

2019 ◽  
Vol 7 (8) ◽  
pp. 1387-1397 ◽  
Author(s):  
Xinfeng Wang ◽  
Ziwen He ◽  
Suhua Shi ◽  
Chung-I Wu
Keyword(s):  
Gene Flow ◽  
Species Concept ◽  
Biological Species ◽  
Biological Species Concept ◽  
Geographical Isolation ◽  
Fundamental Nature ◽  
Genomic Analyses ◽  
Number Of Genes ◽  
The Common ◽  
Common Perception

Abstract The biological species concept (BSC) is the cornerstone of neo-Darwinian thinking. In BSC, species do not exchange genes either during or after speciation. However, as gene flow during speciation is increasingly being reported in a substantial literature, it seems time to reassess the revered, but often doubted, BSC. Contrary to the common perception, BSC should expect substantial gene flow at the onset of speciation, not least because geographical isolation develops gradually. Although BSC does not stipulate how speciation begins, it does require a sustained period of isolation for speciation to complete its course. Evidence against BSC must demonstrate that the observed gene flow does not merely occur at the onset of speciation but continues until its completion. Importantly, recent genomic analyses cannot reject this more realistic version of BSC, although future analyses may still prove it wrong. The ultimate acceptance or rejection of BSC is not merely about a historical debate; rather, it is about the fundamental nature of species – are species (and, hence, divergent adaptations) driven by a relatively small number of genes, or by thousands of them? Many levels of biology, ranging from taxonomy to biodiversity, depend on this resolution.

scholarly journals Sympatric and allopatric differentiation delineates population structure in free-living terrestrial bacteria

2019 ◽  
Author(s):  
Alexander B. Chase ◽  
Philip Arevalo ◽  
Eoin L. Brodie ◽  
Martin F. Polz ◽  
Ulas Karaoz ◽  
...  
Keyword(s):  
Gene Flow ◽  
Isolation By Distance ◽  
Biological Species ◽  
Microbial Populations ◽  
Marker Genes ◽  
Rrna Gene ◽  
Biological Species Concept ◽  
Free Living ◽  
Species Definition ◽  
Isolation By Environment

ABSTRACTIn free-living bacteria and archaea, the equivalent of the biological species concept does not exist, creating several barriers to the study of the processes contributing to microbial diversification. As such, microorganisms are often operationally defined using conserved marker genes (i.e., 16S rRNA gene) or whole-genome measurements (i.e., ANI) to interpret intra-specific processes. However, as in eukaryotes, investigations into microbial populations must consider the potential for interacting genotypes among individuals that are subjected to similar environmental selective pressures. Therefore, we isolated 26 strains within a single bacterial ecotype (equivalent to a eukaryotic species definition) from a common habitat (leaf litter) across a regional climate gradient and asked whether the genetic diversity in a free-living soil bacterium (Curtobacterium) was consistent with patterns of allopatric or sympatric differentiation. By examining patterns of gene flow, our results indicate that microbial populations are delineated by gene flow discontinuities and exhibit evidence for population-specific adaptation. We conclude that the genetic structure within this bacterium is due to both adaptation within localized microenvironments (isolation-by-environment) as well as dispersal limitation between geographic locations (isolation-by-distance).

scholarly journals Hybridization without guilt: gene flow and the biological species concept

2001 ◽  
Vol 14 (6) ◽  
pp. 868-869 ◽  
Author(s):  
H. D. Rundle ◽  
F. Breden ◽  
C. Griswold ◽  
A. ��. Mooers ◽  
R. A. Vos ◽  
...  
Keyword(s):  
Gene Flow ◽  
Species Concept ◽  
Biological Species ◽  
Biological Species Concept

scholarly journals Biological species in the viral world

2018 ◽  
Vol 115 (23) ◽  
pp. 6040-6045 ◽  
Author(s):  
Louis-Marie Bobay ◽  
Howard Ochman
Keyword(s):  
Gene Flow ◽  
Species Concept ◽  
Genome Structure ◽  
Biological Species ◽  
Arbitrary Sequence ◽  
Biological Species Concept ◽  
Host Tropism ◽  
Universal Definition ◽  
Definition Of ◽  
Shared Gene

Due to their dependence on cellular organisms for metabolism and replication, viruses are typically named and assigned to species according to their genome structure and the original host that they infect. But because viruses often infect multiple hosts and the numbers of distinct lineages within a host can be vast, their delineation into species is often dictated by arbitrary sequence thresholds, which are highly inconsistent across lineages. Here we apply an approach to determine the boundaries of viral species based on the detection of gene flow within populations, thereby defining viral species according to the biological species concept (BSC). Despite the potential for gene transfer between highly divergent genomes, viruses, like the cellular organisms they infect, assort into reproductively isolated groups and can be organized into biological species. This approach revealed that BSC-defined viral species are often congruent with the taxonomic partitioning based on shared gene contents and host tropism, and that bacteriophages can similarly be classified in biological species. These results open the possibility to use a single, universal definition of species that is applicable across cellular and acellular lifeforms.

scholarly journals The rate of evolution of postmating-prezygotic reproductive isolation in Drosophila

2017 ◽  
Author(s):  
David A. Turissini ◽  
Joseph A. McGirr ◽  
Sonali S. Patel ◽  
Jean R. David ◽  
Daniel R. Matute
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Hybrid Sterility ◽  
Biological Species ◽  
Biological Species Concept ◽  
Premating Isolation ◽  
Hybrid Inviability ◽  
Systematic Analysis ◽  
Rates Of Evolution ◽  
Postzygotic Barriers

ABSTRACTReproductive isolation (RI) is an intrinsic aspect of species, as described in the Biological Species Concept. For that reason, the identification of the precise traits and mechanisms of RI, and the rates at which they evolve, is crucial to understanding how species originate and persist. Nonetheless, precise measurements of the magnitude of reproductive isolation are rare. Previous work has measured the rates of evolution of prezygotic and postzygotic barriers to gene flow, yet no systematic analysis has carried out the study of the rates of evolution of postmating-prezygotic (PMPZ) barriers. We systematically measured the magnitude of two barriers to gene flow that act after mating occurs but before zygotic fertilization and also measured a premating (female mating rate in nonchoice experiments) and two postzygotic barriers (hybrid inviability and hybrid sterility) for all pairwise crosses of species within the Drosophila melanogaster subgroup. Our results indicate that PMPZ isolation evolves faster than hybrid inviability but slower than premating isolation. We also describe seven new interspecific hybrids in the group. Our findings open up a large repertoire of tools that will enable researchers to manipulate hybrids and explore the genetic basis of interspecific differentiation, reproductive isolation, and speciation.

scholarly journals Toward understanding the genetic mechanisms of speciation: Fine-grained introgressions between species

2020 ◽  
Author(s):  
Xinfeng Wang ◽  
Zixiao Guo ◽  
Shaohua Xu ◽  
Shao Shao ◽  
Sen Li ◽  
...  
Keyword(s):  
Gene Flow ◽  
De Novo ◽  
Biological Species ◽  
Adaptive Divergence ◽  
Biological Species Concept ◽  
Extensive Literature ◽  
Mangrove Species ◽  
Fine Grained ◽  
Genetic Mechanisms ◽  
Definition Of

Abstract The biological species concept (BSC) is the prevailing definition of species whereby genes cannot be exchanged during or after speciation. In contrast, since only genes that contribute to the adaptive divergence between species should be non-exchangeable, BSC appears to bear little relationship to the genetic process of speciation. The rejection of BSC demands evidence of continual gene flow until the completion of speciation. Here, we carry out the sequencing and de novo high-quality assembly of the genomes of two closely related mangrove species (Rhizophora mucronata and R. stylosa). Whole-genome re-sequencing of individuals from their distributions on the tropical coasts shows their genomes to be well delineated in allopatry. They became sympatric in northeastern Australia where their genomes harbor 9,963 and 3,874 introgression blocks, respectively, with each block averaging only about 3-4 Kb. These fine-grained introgressions indicate that gene flow continues even after numerous loci have evolved to become non-introgressable “genomic islets”. Many of these islets, only 1.4 Kb on average, harbor “speciation loci” which contribute to the divergence in flower development or gamete production and thus result in fitness reduction upon introgression. Our fine-grained analysis may thus be the first one to show that gene flow not only happens during speciation, but often continues until the completion of speciation. Under the weight of the extensive literature, BSC may deserve to be retired.

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