Mode Of Divergence Research Articles

Phylogenomic and population genomic analyses reveal the spatial–temporal dynamics of diversification of the Nigella arvensis complex (Ranunculaceae) in the Aegean archipelago

The continental-shelf islands of the Aegean Sea provide an ideal geographical setting for evolutionary-biogeographical studies but disentangling the relationships between palaeogeographical history and the times, orders of modes of taxon divergence is not straightforward. Here, we used phylogenomic and population genomic approaches, based on orthologous gene sequences and transcriptome-derived SNP data, to reconstruct the spatial–temporal evolution of the Aegean Nigella arvensis complex (Ranunculaceae; 11 out of 12 taxa). The group’s early diversification in the Early/Mid-Pliocene (c. 3.77 Mya) resulted in three main lineages (Greek mainland vs. central Aegean + Turkish mainland/eastern Aegean islands), while all extant taxa are of Late Plio-/Early Pleistocene origin (c. 3.30–1.59 Mya). Demographic modelling of the outcrossing taxa uncovered disparate modes of (sub)speciation, including divergence with gene flow on the Greek mainland, para- or peripatric diversification across eastern Aegean islands, and a ‘mixing–isolation–mixing (MIM)’ mode of subspeciation in the Cyclades. The two selfing species (N. stricta, N. doerfleri) evolved independently from the outcrossers. Present-day island configurations are clearly insufficient to explain the spatial–temporal history of lineage diversification and modes of (sub)speciation in Aegean Nigella. Moreover, our identification of positively selected genes in almost all taxa calls into question that this plant group represents a case of ‘non-adaptive’ radiation. Our study revealed an episodic diversification history of the N. arvensis complex, giving new insight into the modes and drivers of island speciation and adaption across multiple spatiotemporal scales.

Delimiting species using DNA and morphological variation in some Alcea (Malvaceae) species based on SRAP markers

Species identification is fundamentally important within the fields of biology, biogeography, ecology and conservation. The genus Alcea (Malvaceae) includes approximately 70 species of mainly Irano-Turanian distribution and is considered one of the most challenging genera of the Middle East, due to its uniformity and pronounced plasticity in morphological traits. In spite vast distribution of many Alcea species that grow in Iraq, there are not any available report on their genetic diversity, mode of divergence and patterns of dispersal. Therefore, we performed molecular (SRAP marker) and morphological studies of 80 accessions from 10 species of Alcea that were collected from different habitats in Iraq. The aims of present study are: 1) can SRAP markers identify Alcea species, 2) what is the genetic structure of these taxa in Iraq, and 3) to investigate the species inter-relationship? The present study revealed that combination of morphological and SRAP data can identify the species.

Population genomics indicate three different modes of divergence and speciation with gene flow in the green-winged teal duck complex

The processes leading to divergence and speciation can differ broadly among taxa with different life histories. We examine these processes in a small clade of ducks with historically uncertain relationships and species limits. The green-winged teal (Anas crecca) complex is a Holarctic species of dabbling duck currently categorized as three subspecies (Anas crecca crecca, A. c. nimia, and A. c. carolinensis) with a close relative, the yellow-billed teal (Anas flavirostris) from South America. A. c. crecca and A. c. carolinensis are seasonal migrants, while the other taxa are sedentary. We examined divergence and speciation patterns in this group, determining their phylogenetic relationships and the presence and levels of gene flow among lineages using both mitochondrial and genome-wide nuclear DNA obtained from 1,393 ultraconserved element (UCE) loci. Phylogenetic relationships using nuclear DNA among these taxa showed A. c. crecca, A. c. nimia, and A. c. carolinensis clustering together to form one polytomous clade, with A. flavirostris sister to this clade. This relationship can be summarized as (crecca, nimia, carolinensis)(flavirostris). However, whole mitogenomes revealed a different phylogeny: (crecca, nimia)(carolinensis, flavirostris). The best demographic model for key pairwise comparisons supported divergence with gene flow as the probable speciation mechanism in all three contrasts (crecca−nimia, crecca−carolinensis, and carolinensis−flavirostris). Given prior work, gene flow was expected among the Holarctic taxa, but gene flow between North American carolinensis and South American flavirostris (M ∼0.1–0.4 individuals/generation), albeit low, was not expected. Three geographically oriented modes of divergence are likely involved in the diversification of this complex: heteropatric (crecca−nimia), parapatric (crecca−carolinensis), and (mostly) allopatric (carolinensis−flavirostris). Our study shows that ultraconserved elements are a powerful tool for simultaneously studying systematics and population genomics in systems with historically uncertain relationships and species limits.

Global phylogeography of hyperdiverse lanternfishes indicates sympatric speciation in the deep sea

AbstractAimLanternfishes (Myctophidae) are one of the most species‐rich families of mid‐water fishes. They inhabit the mesopelagic zone, where physical barriers to dispersal and gene flow are permeable. Thus, modes of speciation that rely exclusively on geographical separation are potentially of less importance than those that rely more prominently on evolution of assortative mating through divergent habitat use and/or sexual signals, including visual signals from bioluminescent light organs. Here we used phylogenetic, ecological and morphological data to investigate the roles of geography, habitat use and lateral photophores in lanternfish speciation.LocationGlobal.Time periodData collected between 1950 and 2015.Major taxa studiedLanternfishes (Myctophidae).MethodsEcological niche models (ENMs) were developed for 167 species, enabling the community composition of 33 mesopelagic ecoregions to be determined. Sequence data for seven protein‐coding regions from 175 species were used to reconstruct a phylogenetic tree of Myctophidae. Age‐overlap correlation tests were conducted using this phylogeny with outputs from ENMs (pairwise geographical overlap and pairwise ecological niche overlap, n = 136), in addition to matrices of pairwise depth overlap (n = 158) and photophore pattern dissimilarity (n = 161).ResultsCommunities assembled according to nine broad climatic regions, and recently diverged species pairs possessed greater geographical and ecological niche overlap than more distantly related species, indicating that sympatric or parapatric speciation might be dominant modes of divergence. Differences in photophore patterns increased with the relative age of speciation events, suggesting that photophore patterns are largely constrained by phylogeny.Main conclusionsBased on this evidence, we suggest that large‐scale oceanographic features structure the diversity of lanternfish communities and that speciation within this family of deep‐water fishes might not have required geographical isolation.

Diodonopteris virgulata sp. nov., a climbing fern from the early Permian Wuda Tuff Flora and its paleoecology

Botryopteridaceae, characterized by an omega-shaped foliar trace, is one of the best known late Paleozoic fern families with frequent occurrence in the Carboniferous of Euramerica and recent recognition in Permian deposits of Gondwana and Cathaysia. Diodonopteris is a recently established botryopterid genus based on coal-ball material from the lower Permian Taiyuan Formation of Shanxi Province, China. Here, a new species of Diodonopteris is described based on an anatomically preserved specimen from the well-known early Permian Wuda Tuff Flora in the Wuda Coalfield of Inner Mongolia, China. Diodonopteris virgulata sp. nov. is similar to the type species D. gracilis in the marginal position of protoxylem groups but differs from the latter in having a simpler cortex and a more expanded xylem strand. The two known Diodonopteris species share several characteristics considered ancestral among botryopterids, including strand shape, mode of pinna trace divergence, weak pinnule lamination, and a laminar wing on the rachis, as is consistent with Diodonopteris sitting outside any of the derived sublineages within Botryopteris. D. virgulata is confirmed to be a climber by direct preservation with the host. Moreover, the host plant is also evidenced to be a climber. The repeated preservation of the dual-climbing phenomenon in this swamp forest signals the complexity of early Permian ecosystems.

Review of the Gargara genistae (Fabricius, 1775) species group (Hemiptera: Membracidae) from Russia and adjacent territories.

In Russia, Kazakhstan, and Central Asia the Gargara genistae species group includes three species differing from each other in the male calling signal patterns, but almost indistinguishable in external appearance and the male genitalia shape. Illustrated descriptions of morphology and the male calling signals, and data on host plants and distribution for all species are given. Considerations concerning possible modes of species divergence in this group are provided.

Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulum Complex).

Many phylogeographic studies on species with large ranges have found genetic-geographic structure associated with changes in habitat and physical barriers preventing or reducing gene flow. These interactions with geographic space, contemporary and historical climate, and biogeographic barriers have complex effects on contemporary population genetic structure and processes of speciation. While allopatric speciation at biogeographic barriers is considered the primary mechanism for generating species, more recently it has been shown that parapatric modes of divergence may be equally or even more common. With genomic data and better modeling capabilities, we can more clearly define causes of speciation in relation to biogeography and migration between lineages, the location of hybrid zones with respect to the ecology of parental lineages, and differential introgression of genes between taxa. Here, we examine the origins of three Nearctic milksnakes (Lampropeltis elapsoides, Lampropeltis triangulum and Lampropeltis gentilis) using genome-scale data to better understand species diversification. Results from artificial neural networks show that a mix of a strong biogeographic barrier, environmental changes, and physical space has affected genetic structure in these taxa. These results underscore conspicuous environmental changes that occur as the sister taxa L. triangulum and L. gentilis diverged near the Great Plains into the forested regions of the Eastern Nearctic. This area has been recognized as a region for turnover for many vertebrate species, but as we show here the contemporary boundary does not isolate these sister species. These two species likely formed in the mid-Pleistocene and have remained partially reproductively isolated over much of this time, showing differential introgression of loci. We also demonstrate that when L. triangulum and L. gentilis are each in contact with the much older L. elapsoides, some limited gene flow has occurred. Given the strong agreement between nuclear and mtDNA genomes, along with estimates of ecological niche, we suggest that all three lineages should continue to be recognized as unique species. Furthermore, this work emphasizes the importance of considering complex modes of divergence and differential allelic introgression over a complex landscape when testing mechanisms of speciation. [Cline; delimitation; Eastern Nearctic; Great Plains; hybrids; introgression; speciation.].

Punctuated evolution in the learned songs of African sunbirds.

Learned traits are thought to be subject to different evolutionary dynamics than other phenotypes, but their evolutionary tempo and mode has received little attention. Learned bird song has been thought to be subject to rapid and constant evolution. However, we know little about the evolutionary modes of learned song divergence over long timescales. Here, we provide evidence that aspects of the territorial songs of Eastern Afromontane sky island sunbirds Cinnyris evolve in a punctuated fashion, with periods of stasis of the order of hundreds of thousands of years or more, broken up by evolutionary pulses. Stasis in learned songs is inconsistent with learned traits being subject to constant or frequent change, as would be expected if selection does not constrain song phenotypes over evolutionary timescales. Learned song may instead follow a process resembling peak shifts on adaptive landscapes. While much research has focused on the potential for rapid evolution in bird song, our results suggest that selection can tightly constrain the evolution of learned songs over long timescales. More broadly, these results demonstrate that some aspects of highly variable, plastic traits can exhibit punctuated evolution, with stasis over long time periods.

Multiple paths to morphological diversification during the origin of amniotes.

Early terrestrial vertebrates (amniotes) provide a classic example of diversification following adaptive zone invasion. The initial terrestrialization of vertebrates was closely followed by dietary diversification, as evidenced by a proliferation of craniomandibular and dental adaptations. However, morphological evolution of early amniotes has received limited study, in analyses with restricted taxonomic scope, leaving substantial questions about the dynamics of this important terrestrial radiation. We use novel analyses of discrete characters to quantify variation in evolutionary rates and constraints during diversification of the amniote feeding apparatus. We find evidence for an early burst, comprising high rates of anatomical change that decelerated through time, giving way to a background of saturated morphological evolution. Subsequent expansions of phenotypic diversity were not associated with increased evolutionary rates. Instead, variation in the mode of evolution became important, with groups representing independent origins of herbivory evolving distinctive, group-specific morphologies and thereby exploring novel character-state spaces. Our findings indicate the importance of plant-animal interactions in structuring the earliest radiation of amniotes and demonstrate the importance of variation in modes of phenotypic divergence during a major evolutionary radiation.

The mode of expression divergence in Drosophila fat body is infection-specific.

Transcription is controlled by interactions of cis-acting DNA elements with diffusible trans-acting factors. Changes in cis or trans factors can drive expression divergence within and between species, and their relative prevalence can reveal the evolutionary history and pressures that drive expression variation. Previous work delineating the mode of expression divergence in animals has largely used whole-body expression measurements in one condition. Because cis-acting elements often drive expression in a subset of cell types or conditions, these measurements may not capture the complete contribution of cis-acting changes. Here, we quantify the mode of expression divergence in the Drosophila fat body, the primary immune organ, in several conditions, using two geographically distinct lines of D. melanogaster and their F1 hybrids. We measured expression in the absence of infection and in infections with Gram-negative S. marcescens or Gram-positive E. faecalis bacteria, which trigger the two primary signaling pathways in the Drosophila innate immune response. The mode of expression divergence strongly depends on the condition, with trans-acting effects dominating in response to Gram-negative infection and cis-acting effects dominating in Gram-positive and preinfection conditions. Expression divergence in several receptor proteins may underlie the infection-specific trans effects. Before infection, when the fat body has a metabolic role, there are many compensatory effects, changes in cis and trans that counteract each other to maintain expression levels. This work shows that within a single tissue, the mode of expression divergence varies between conditions and suggests that these differences reflect the diverse evolutionary histories of host–pathogen interactions.

Strong genetic differentiation of the Paracaryum species (Boraginaceae) detected by inter-simple sequence repeats (ISSR)

Species identification is fundamentally important within the fields of biology, biogeography, ecology and conservation. The genus Paracaryum belongs to tribe Cynoglosseae of the family Boraginaceae is a herbaceous genus including approximately 67 species, mostly distributed in the Irano-Turanian phytogeographical region. In spite vast distribution of many Paracaryum species that grow in different habitats, there are not any available report on their genetic diversity, mode of divergence and patterns of dispersal. Therefore, we performed molecular (ISSR markers) of 98 accessions from 12 species of Paracaryum that were collected from different habitats. A set of 10 ISSR markers was used. The genetic distances were estimated based on Jaccard similarity coefficient and the descriptive statistics of populations for estimation of genetic parameters were also performed. A total of 90 polymorphic bands were obtained. The present study revealed that ISSR data can delimit the species. AMOVA and STRUCTURE analysis revealed that the species of Paracaryum belongs are genetically differentiated but have some degree of shared common alleles.

Inter-simple sequence repeats genetic relationships between populations of Consolida (Ranunculaceae)

In fields like ecology, biogeography, conservation biology, and macroevolutionary theory, species are considered as the fundamental unit of study. Gray (1821), an expert on British flora, regarded the genus Consolida to be a distinct genus based on a single species (C. regalis). Consolida, on the other hand, is believed by some scholars to be a part of Delphinium. There are no reports on the genetic diversity, modes of divergence, or dispersion patterns of the various Consolida species that grow in Iran despite their widespread distribution. Hence, a combination of atomic (ISSR markers) and morphological examinations of 78 increases from seven species of Consolida were conducted. One goal of this work is to determine the diagnostic usefulness of ISSR markers in the delimitation of Consolida species, another is to determine the genetic structure of these taxa, and a third is to look at the relationships between species within these groups. It was discovered in the current research that combining morphological and ISSR data may help identify species. Analysis using AMOVA and STRUCTURE found that the species of Consolida are genetically distinct, yet have some common genes.

Genetic diversity and population structure analysis in Lonicera L. (Caprifoliaceae) with the use of ISSR molecular markers

Species delimitation is essential since species is regarded as the basic unit of analysis in nearly all biological disciplines, such as ecology, biogeography, conservation biology, and macroevolution. The genus Lonicera, which includes approximately 200 species, is a major component of the family Caprifoliaceae, comprising a large number of horticultural and economically important shrubs and tree species. This genus is represented in Iran by 9 species. In spite vast distribution of many Lonicera species that grow in Iran, there are not any available report on their genetic diversity, mode of divergence and patterns of dispersal. Therefore data molecular (ISSR markers) with four primer pairs generated 77 polymorphic bands and morphological studies of 70 accessions from 7 species of Lonicera, that were collected from different habitats in Iran were performed. The aims of the present study are: 1) to find the diagnostic value of ISSR markers in delimitation of Lonicera species, 2) to find the genetic structure of these taxa in Iran, and 3) to investigate the .species inter-relationship. The present study revealed that combination of morphological and ISSR data can delimit the species. AMOVA and STRUCTURE analysis revealed that the species of Lonicera are genetically differentiated but have some degree of shared common alleles.

The geometry and genetics of hybridization.

When divergent populations form hybrids, hybrid fitness can vary with genome composition, current environmental conditions, and the divergence history of the populations. We develop analytical predictions for hybrid fitness, which incorporate all three factors. The predictions are based on Fisher's geometric model, and apply to a wide range of population genetic parameter regimes and divergence conditions, including allopatry and parapatry, local adaptation, and drift. Results show that hybrid fitness can be decomposed into intrinsic effects of admixture and heterozygosity, and extrinsic effects of the (local) adaptedness of the parental lines. Effect sizes are determined by a handful of geometric distances, which have a simple biological interpretation. These distances also reflect the mode and amount of divergence, such that there is convergence toward a characteristic pattern of intrinsic isolation. We next connect our results to the quantitative genetics of line crosses in variable or patchy environments. This means that the geometrical distances can be estimated from cross data, and provides a simple interpretation of the “composite effects.” Finally, we develop extensions to the model, involving selectively induced disequilibria, and variable phenotypic dominance. The geometry of fitness landscapes provides a unifying framework for understanding speciation, and wider patterns of hybrid fitness.

Evidence for spatial clines and mixed geographic modes of speciation for North American cherry-infesting Rhagoletis (Diptera: Tephritidae) flies.

An important criterion for understanding speciation is the geographic context of population divergence. Three major modes of allopatric, parapatric, and sympatric speciation define the extent of spatial overlap and gene flow between diverging populations. However, mixed modes of speciation are also possible, whereby populations experience periods of allopatry, parapatry, and/or sympatry at different times as they diverge. Here, we report clinal patterns of variation for 21 nuclear‐encoded microsatellites and a wing spot phenotype for cherry‐infesting Rhagoletis (Diptera: Tephritidae) across North America consistent with these flies having initially diverged in parapatry followed by a period of allopatric differentiation in the early Holocene. However, mitochondrial DNA (mtDNA) displays a different pattern; cherry flies at the ends of the clines in the eastern USA and Pacific Northwest share identical haplotypes, while centrally located populations in the southwestern USA and Mexico possess a different haplotype. We hypothesize that the mitochondrial difference could be due to lineage sorting but more likely reflects a selective sweep of a favorable mtDNA variant or the spread of an endosymbiont. The estimated divergence time for mtDNA suggests possible past allopatry, secondary contact, and subsequent isolation between USA and Mexican fly populations initiated before the Wisconsin glaciation. Thus, the current genetics of cherry flies may involve different mixed modes of divergence occurring in different portions of the fly's range. We discuss the need for additional DNA sequencing and quantification of prezygotic and postzygotic reproductive isolation to verify the multiple mixed‐mode hypothesis for cherry flies and draw parallels from other systems to assess the generality that speciation may commonly involve complex biogeographies of varying combinations of allopatric, parapatric, and sympatric divergence.

Divergence, gene flow, and speciation in eight lineages of trans-Beringian birds.

Determining how genetic diversity is structured between populations that span the divergence continuum from populations to biological species is key to understanding the generation and maintenance of biodiversity. We investigated genetic divergence and gene flow in eight lineages of birds with a trans-Beringian distribution, where Asian and North American populations have likely been split and reunited through multiple Pleistocene glacial cycles. Our study transects the speciation process, including eight pairwise comparisons in three orders (ducks, shorebirds and passerines) at population, subspecies and species levels. Using ultraconserved elements (UCEs), we found that these lineages represent conditions from slightly differentiated populations to full biological species. Although allopatric speciation is considered the predominant mode of divergence in birds, all of our best divergence models included gene flow, supporting speciation with gene flow as the predominant mode in Beringia. In our eight lineages, three were best described by a split-migration model (divergence with gene flow), three best fit a secondary contact scenario (isolation followed by gene flow), and two showed support for both models. The lineages were not evenly distributed across a divergence space defined by gene flow (M) and differentiation (FST ), instead forming two discontinuous groups: one with relatively shallow divergence, no fixed single nucleotide polymorphisms (SNPs), and high rates of gene flow between populations; and the second with relatively deeply divergent lineages, multiple fixed SNPs, and low gene flow. Our results highlight the important role that gene flow plays in avian divergence in Beringia.

Revisiting a Landmark Study System: No Evidence for a Punctuated Mode of Evolution in Metrarabdotos.

Is speciation generally a "special time" in morphological evolution, or are lineage-splitting events just "more of the same" where the end product happens to be two separate lineages? Data on evolutionary dynamics during anagenetic and cladogenetic events among closely related lineages within a clade are rare, but the fossil record of the bryozoan genus Metrarabdotos is considered a textbook example of a clade where speciation causes rapid evolutionary change against a backdrop of morphological stasis within lineages. Here, we point to some methodological and measurement theoretical issues in the original work on Metrarabdotos. We then reanalyze a subset of the original data that can be meaningfully investigated using quantitative statistical approaches similar to those used in the original studies. We consistently fail to find variation in the evolutionary process during within-lineage evolution compared with cladogenetic events: the rates of evolution, the strength of selection, and the directions traveled in multivariate morphospace are not different when comparing evolution within lineages and at speciation events in Metrarabdotos, and genetic drift cannot be excluded as a sufficient explanation for the morphological differentiation within lineages and during speciation. Although widely considered the best example of a punctuated mode of evolution, morphological divergence and speciation are not linked in Metrarabdotos.

Tempo and mode of allopatric divergence in the weakly electric fish Sternopygus dariensis in the Isthmus of Panama

Spatial isolation is one of the main drivers of allopatric speciation, but the extent to which spatially-segregated populations accumulate genetic differences relevant to speciation is not always clear. We used data from ultraconserved elements (UCEs) and whole mitochondrial genomes (i.e., mitogenomes) to explore genetic variation among allopatric populations of the weakly electric fish Sternopygus dariensis across the Isthmus of Panama. We found strong genetic divergence between eastern and western populations of S. dariensis. Over 77% of the UCE loci examined were differentially fixed between populations, and these loci appear to be distributed across the species’ genome. Population divergence occurred within the last 1.1 million years, perhaps due to global glaciation oscillations during the Pleistocene. Our results are consistent with a pattern of genetic differentiation under strict geographic isolation, and suggest the presence of incipient allopatric species within S. dariensis. Genetic divergence in S. dariensis likely occurred in situ, long after the closure of the Isthmus of Panama. Our study highlights the contribution of spatial isolation and vicariance to promoting rapid diversification in Neotropical freshwater fishes. The study of spatially-segregated populations within the Isthmus of Panama could reveal how genetic differences accumulate as allopatric speciation proceeds.

Phylogeny, ancestors, and anagenesis in the hominin fossil record

AbstractProbabilistic approaches to phylogenetic inference have recently gained traction in paleontological studies. Because they directly model processes of evolutionary change, probabilistic methods facilitate a deeper assessment of variability in evolutionary patterns by weighing evidence for competing models. Although phylogenetic methods used in paleontological studies have generally assumed that evolution proceeds by splitting cladogenesis, extensions to previous models help explore the potential for morphological and temporal data to provide differential support for contrasting modes of evolutionary divergence. Recent methodological developments have integrated ancestral relationships into probabilistic phylogenetic methods. These new approaches rely on parameter-rich models and sophisticated inferential methods, potentially obscuring the respective contributions of data and models. In this study, we describe a simple likelihoodist approach that combines probabilistic models of morphological evolution and fossil preservation to reconstruct both cladogenetic and anagenetic relationships. By applying this approach to a data set of fossil hominins, we demonstrate the capability of existing models to unveil evidence for anagenesis presented by morphological and temporal data. This evidence was previously recognized by qualitative assessments, but largely ignored by quantitative phylogenetic analyses. For example, we find support for directly ancestral relationships in multiple lineages:Sahelanthropusis ancestral to later hominins;Australopithecus anamensisis ancestral toAustralopithecus afarensis;Australopithecus garhiis ancestral toHomo;Homo antecessoris ancestral toHomo heidelbergensis, which in turn is ancestral to bothHomo sapiensandHomo neanderthalensis. By accommodating direct ancestry in phylogenetics, quantitative results align more closely with previous qualitative expectations.

Phylogeography of a widespread lizard complex reflects patterns of both geographic and ecological isolation.

A primary challenge for modern phylogeography is understanding how ecology and geography, both contemporary and historical, shape the spatial distribution and evolutionary histories of species. Phylogeographic patterns are the result of many factors, including geology, climate, habitat, colonization history and lineage-specific constraints. Assessing the relative influences of these factors is difficult because few species, regions and environments are sampled in enough detail to compare competing hypotheses rigorously and because a particular phylogeographic pattern can potentially result from different evolutionary scenarios. The silky anoles (Anolis sericeus complex) of Central America and Mexico are abundant and found in all types of lowland terrestrial habitat, offering an excellent opportunity to test the relative influences of the factors affecting diversification. Here, we performed a range-wide statistical phylogeographic analysis on restriction site-associated DNA (RAD) markers from silky anoles and compared the phylogeographic patterns we recovered to historical and contemporary environmental and topographic data. We constructed niche models to compare niche overlap between sister lineages and conducted coalescent simulations to characterize how the major lineages of silky anoles have diverged. Our results revealed that the mode of divergence for major lineage diversification events was geographic isolation, resulting in ecological divergence between lineages, followed by secondary contact. Moreover, comparisons of parapatric sister lineages suggest that ecological niche divergence contributed to isolation by environment in this system, reflecting the natural history differences among populations in divergent environments.