skip to main content


Title: Taxonomic challenges posed by discordant evolutionary scenarios supported by molecular and morphological data in the Amazonian Synallaxis rutilans group (Aves: Furnariidae)
Abstract

Alpha taxonomy endeavours to propose a coherent vision of existing species and, simultaneously, to individualize the natural entities useful to understand evolutionary processes. This ideal is especially difficult when available data lack congruence. Here we address the polytypic species Synallaxis rutilans (ruddy spinetail), a suboscine passerine widely distributed in the Amazon Basin and whose taxonomy could, potentially, aid our understanding of processes shaping its biodiversity. Combining genetic [genomic ultraconserved elements (UCE) and mtDNA] and morphological data, we demonstrate that while delimitation of genetic lineages and their phylogenetic relationships are strongly associated with classic Amazonian geographic barriers, such as rivers, different coloration patterns appear to be more associated with local selection processes for phenotype. Employing an evolutionary approach, whereby the species is considered a taxonomic category, rather than a nomenclatural rank, we propose to recognize five species: S. amazonica, S. caquetensis, S. dissors, S. omissa and S. rutilans. The taxonomic arrangement proposed here permits better understanding of the similarities and differences among taxa from different areas of endemism, and represents patterns of genetic and morphological diversity resulting from distinct processes acting across certain time frames. This arrangement draws attention to the importance of understanding the evolutionary processes operating in the complex and constantly changing Amazonian landscape.

 
more » « less
NSF-PAR ID:
10474564
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ;
Publisher / Repository:
Oxford University Press
Date Published:
Journal Name:
Zoological Journal of the Linnean Society
Volume:
195
Issue:
1
ISSN:
0024-4082
Format(s):
Medium: X Size: p. 65-87
Size(s):
["p. 65-87"]
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    Taxonomic data is essential to advance the discovery and description of biodiversity, as well as the study of evolutionary processes. Emerging large-scale datasets and new methods of analysis have provided different approaches to describe biodiversity. Here, we present a review of the taxonomic history in Cycadales including an analysis of historical taxonomic concepts and approaches used for species delimitation. We examine the trends in the publication of new species following taxonomic works in books, journals and horticultural catalogues, monographic projects and floras where species treatments were published. In addition, we review the studies concerning species delimitations using the literature available in scientific journals appearing in the database ISI Web of Knowledge. The approaches used were discussed throughout all research focused on empirical and theoretical considerations in each study. We review the current state of the studies on causal processes that have given rise to the currently recognized diversity. The trend shows that taxonomic work on discovery and description of species has been intensive in the last 40 years culminating in 38.8% of binomials published. As a result, we consider the relevance of the monographs and floras for identification of species for other biological disciplines and the content of these contributions is compared and discussed. A total of six criteria (diagnosability, phenetic, phylogenetic, genotypic cluster, niche specialization and coalescent) were detected from the following three approaches to species delimitation within Cycadales: traditional, integrative taxonomy, and monophyletic. In all cases, the results from these species delimitations not only provided a taxonomic treatment or proposed a new species, but also supposedly clarified the other species involved as a result of the new taxonomic concept of the new species described. Most investigations of species delimitation used the traditional approach or a phenetic criteria. Finally, we discuss evolutionary studies on causal processes involved in cycad diversity. This is considered in the context of species delimitation as hypothesis testing for a successful evaluation of variation in both genetic and morphological understanding.

     
    more » « less
  2. Abstract

    Understanding the processes that drive divergence within and among species is a long‐standing goal in evolutionary biology. Traditional approaches to assessing differentiation rely on phenotypes to identify intra‐ and interspecific variation, but many species express subtle morphological gradients in which boundaries among forms are unclear. This intraspecific variation may be driven by differential adaptation to local conditions and may thereby reflect the evolutionary potential within a species. Here, we combine genetic and morphological data to evaluate intraspecific variation within the Nelson's (Ammodramus nelsoni) and salt marsh (Ammodramus caudacutus) sparrow complex, a group with populations that span considerable geographic distributions and a habitat gradient. We evaluated genetic structure among and within five putative subspecies ofA. nelsoniandA. caudacutususing a reduced‐representation sequencing approach to generate a panel of 1929SNPs among 69 individuals. Although we detected morphological differences among some groups, individuals sorted along a continuous phenotypic gradient. In contrast, the genetic data identified three distinct clusters corresponding to populations that inhabit coastal salt marsh, interior freshwater marsh and coastal brackish–water marsh habitats. These patterns support the current species‐level recognition but do not match the subspecies‐level taxonomy within each species—a finding which may have important conservation implications. We identified loci exhibiting patterns of elevated divergence among and within these species, indicating a role for local selective pressures in driving patterns of differentiation across the complex. We conclude that this evidence for adaptive variation among subspecies warrants the consideration of evolutionary potential and genetic novelty when identifying conservation units for this group.

     
    more » « less
  3. Abstract

    Several factors have been proposed as drivers of species diversification in the Neotropics, including environmental heterogeneity, the development of drainage systems and historical changes in forest distribution due to climatic oscillations. Here, we investigate which drivers contributed to the evolutionary history and current patterns of diversity of a polymorphic songbird (Arremon taciturnus) that is widely distributed in Amazonian and Atlantic forests as well as in Cerrado gallery and seasonally‐dry forests. We use genomic, phenotypic and habitat heterogeneity data coupled with climatic niche modelling. Results suggest the evolutionary history of the species is mainly related to paleoclimatic changes, although changes in the strength of the Amazon river as a barrier to dispersal, current habitat heterogeneity and geographic distance were also relevant. We propose an ancestral distribution in the Guyana Shield, and recent colonization of areas south of the Amazon river at ~380 to 166 kya, and expansion of the distribution to southern Amazonia, Cerrado and the Atlantic Forest. Since then, populations south of the Amazon River have been subjected to cycles of isolation and possibly secondary contact due to climatic changes that affected habitat heterogeneity and population connectivity. Most Amazonian rivers are not associated with long lasting isolation of populations, but some might act as secondary barriers, susceptible to crossing under specific climatic conditions. Morphological variation, while stable in some parts of the distribution, is not a reliable indicator of genetic structure or phylogenetic relationships.

     
    more » « less
  4. Abstract Aim

    To investigate the cryptic diversity and diversification timing in the putatively low‐dispersal Amazonian leaf‐litter lizardLoxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation.

    Location

    Central Amazonia, Brazil.

    Taxon

    Squamata; Gymnophthalmidae;Loxopholis osvaldoi.

    Methods

    We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with *BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographical distance among localities, the environment and the position of localities in relation to main rivers were tested by redundancy analysis (RDA).

    Results

    We detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE or historical factors.

    Main Conclusions

    Our results strongly suggest thatL.osvaldoiis a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history ofL.osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that nonlinear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.

     
    more » « less
  5. Abstract

    Significant advances have been made in species delimitation and numerous methods can test precisely defined models of speciation, though the synthesis of phylogeography and taxonomy is still sometimes incomplete. Emerging consensus treats distinct genealogical clusters in genome-scale data as strong initial evidence of speciation in most cases, a hypothesis that must therefore be falsified under an explicit evolutionary model. We can now test speciation hypotheses linking trait differentiation to specific mechanisms of divergence with increasingly large data sets. Integrative taxonomy can, therefore, reflect an understanding of how each axis of variation relates to underlying speciation processes, with nomenclature for distinct evolutionary lineages. We illustrate this approach here with Seal Salamanders (Desmognathus monticola) and introduce a new unsupervised machine-learning approach for species delimitation. Plethodontid salamanders are renowned for their morphological conservatism despite extensive phylogeographic divergence. We discover 2 geographic genetic clusters, for which demographic and spatial models of ecology and gene flow provide robust support for ecogeographic speciation despite limited phenotypic divergence. These data are integrated under evolutionary mechanisms (e.g., spatially localized gene flow with reduced migration) and reflected in emergent properties expected under models of reinforcement (e.g., ethological isolation and selection against hybrids). Their genetic divergence is prima facie evidence for species-level distinctiveness, supported by speciation models and divergence along axes such as behavior, geography, and climate that suggest an ecological basis with subsequent reinforcement through prezygotic isolation. As data sets grow more comprehensive, species-delimitation models can be tested, rejected, or corroborated as explicit speciation hypotheses, providing for reciprocal illumination of evolutionary processes and integrative taxonomies. [Desmognathus; integrative taxonomy; machine learning; species delimitation.]

     
    more » « less