PACT in practice: comparative historical biogeographic patterns and species–area relationships of the Greater Antillean and Hawaiian Island terrestrial biotas

Aim To compare the evolutionary and ecological patterns of two extensively studied island biotas with differing geological histories (the Hawaiian Islands and the Greater Antilles). We evaluated the results from PACT (phylogenetic analysis for comparing trees), an innovative approach that has been proposed to reveal general patterns of biotic expansion (between regions) and in situ (within a region) diversification, as well as species–area relationships (SAR) and the taxon pulse dynamic. Location The Hawaiian Islands and Greater Antilles. Methods We used the PACT algorithm to construct general area cladograms and identified biotic expansion and in situ nodes. We analysed the power‐law SAR and relative contribution of biotic expansion and in situ diversification events using power‐law and linear regression analyses. Results Both biotic expansion and in situ nodes were prevalent throughout the PACT general area cladograms (Greater Antilles, 55.9% biotic expansion, 44.1% in situ; Hawaiian Islands, 40.6% biotic expansion, 59.4% in situ). Of the biotic expansion events, both forward and backward events occurred in both regions (Greater Antilles, 85.1% forward, 14.9% backward; Hawaiian Islands, 65% forward, 35% backward). Additionally, there is a power‐law SAR for the Greater Antilles but not for the Hawaiian Islands. However, exclusion of Hawai'i (the youngest, largest Hawaiian Island) produced a power‐law SAR for the Hawaiian Islands. Main conclusions The prevalence of in situ events as well as forward and backward biotic expansion events reveals that both Hawaiian and Greater Antillean biotas have evolved through alternating episodes of biotic expansion and in situ diversification. These patterns are characteristic of the taxon pulse dynamic, for which few data have previously been recorded on islands. Additionally, our analysis revealed that historical influences on the power‐law SARs are pronounced in both assemblages: old, small islands are relatively species rich and young, large islands are relatively species poor. Thus, our PACT results are consistent with hypotheses of geological influence on the evolution of island biotas and also provide greater insight into the role of the taxon pulse dynamic in the formation of island equilibria.     

West to east dispersal and subsequent rapid diversification of the mega‐diverse genus Begonia (Begoniaceae) in the Malesian archipelago

Aim The complex palaeogeography of the Malesian archipelago, characterized by the evolution of an ever‐changing mosaic of terrestrial and marine areas throughout the Cenozoic, provides the geographic backdrop for the remarkable diversification of Malesian Begonia (> 450 species). This study aimed to investigate the origin of Malesian Begonia, the directionality of dispersal events within the Malesian archipelago and the impact of ancient water gaps on colonization patterns, and to identify drivers of diversification. Location Asia, Southeast Asia, Malesia. Methods Plastid DNA sequence data of representatives of all families of the Cucurbitales and Fagales (matK, rbcL, trnL intron, trnL–F spacer, 4076 aligned positions, 92 taxa) and a sample of all major Asian Begonia sections (ndhA intron, ndhF–rpl32 spacer, rpl32–trnL spacer, 4059 aligned positions, 112 taxa) were analysed under an uncorrelated‐rates relaxed molecular clock model to estimate the age of the Begonia crown group divergence and divergence ages within Asian Begonia. Ancestral areas were reconstructed using a likelihood approach implementing a dispersal–extinction–cladogenesis model, and with a Bayesian approach to dispersal–vicariance analysis. Results The results indicated an initial diversification of Asian Begonia in continental Asia in the Miocene, and subsequent colonization of Malesia by multiple lineages. There was support for at least six independent dispersal events from continental Asia and western Malesia to Wallacea dating from the late Miocene to the Pleistocene. Begonia section Petermannia (> 270 species) originated in Western Malesia, and subsequently dispersed to Wallacea, New Guinea and the Philippines. Lineages within this section diversified rapidly since the Pliocene, coinciding with rapid orogenesis on Sulawesi and New Guinea. Main conclusions The predominant trend of Begonia dispersals between continental Asia and Malesia, and also within Malesia, has been from west to east. The water bodies separating the Sunda Shelf region from Wallacea have been porous barriers to dispersal in Begonia following the emergence of substantial land in eastern Malesia from the late Miocene onwards. We hypothesize two major drivers of the diversification of Malesian Begonia: (1) the formation of topographical heterogeneity and the promotion of microallopatry by orogenesis in the Pliocene and Pleistocene; and (2) cyclic vicariance by frequent habitat fragmentations and amalgamations due to climate and sea‐level fluctuations during the Pleistocene.     

Island biogeography of Caribbean coral reef fish

Aim The goal of our study was to test fundamental predictions of biogeographical theories in tropical reef fish assemblages, in particular relationships between fish species richness and island area, isolation and oceanographic variables (temperature and productivity) in the insular Caribbean. These analyses complement an analogous and more voluminous body of work from the tropical Indo‐Pacific. The Caribbean is more limited in area with smaller inter‐island distances than the Indo‐Pacific, providing a unique context to consider fundamental processes likely to affect richness patterns of reef fish. Location Caribbean Sea. Methods We compiled a set of data describing reef‐associated fish assemblages from 24 island nations across the Caribbean Sea, representing a wide range of isolation and varying in land area from 53 to 110,860 km². Regression‐based analyses compared the univariate and combined effects of island‐specific physical predictors on fish species richness. Results We found that diversity of reef‐associated fishes increases strongly with increasing island area and with decreasing isolation. Richness also increases with increasing nearshore productivity. Analyses of various subsets of the entire data set reveal the robustness of the richness data and biogeographical patterns. Main conclusions Within the relatively small and densely packed Caribbean basin, fish species richness fits the classical species–area relationship. Richness also was related negatively to isolation, suggesting direct effects of dispersal limitation in community assembly. Because oceanic productivity was correlated with isolation, however, the related effects of system‐wide productivity on richness cannot be disentangled. These results highlight fundamental mechanisms that underlie spatial patterns of biodiversity among Caribbean coral reefs, and which are probably also are functioning in the more widespread and heterogeneous reefs of the Indo‐Pacific.     

Phylogeographic analysis of the nocturnal velvet ant genus Dilophotopsis (Hymenoptera: Mutillidae) provides insights into diversification in the Nearctic deserts

Understanding the history of diversification in the North American deserts has long been a goal of biogeographers and evolutionary biologists. Although it appears that a consensus is forming regarding the patterns of diversification in the Nearctic deserts in vertebrate taxa, little work has been done exploring the historical biogeography of widespread invertebrate taxa. Before a robust model of geobiotic change in the North American deserts can be proposed, it needs to be determined whether the same historical events affected vertebrate and invertebrate taxa in the same way. We explore the phylogeographic patterns in a widespread nocturnal wasp genus Dilophotopsis using two rDNA loci, the internal transcribed spacer regions 1 and 2 (ITS1 and ITS2). We use Bayesian phylogenetic analysis and haplotype network analysis to determine whether a consistent geographic pattern exists among species and populations within Dilophotopsis. We also used molecular dating techniques to estimate divergence dates of the major phylogenetic clades. Our analyses indicates that the species‐level divergences in Dilophotopsis occurred in the Neogene, and likely were driven by mountain building during the Miocene–Pliocene boundary (approximately 5 Mya) similar to the divergences in many vertebrate taxa. The population‐level divergences within species occurred during the Pleistocene (0.1–1.8 Mya). The present study shows that similar patterns of diversification exist in vertebrate and invertebrate taxa. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 360–375.     

Time and space in biogeography: response to Parenti & Ebach (2013)

A recent Guest Editorial by Parenti & Ebach (2013, Journal of Biogeography, 40, 813–820) disagrees with the methods or interpretations in two of our recent papers. In addition, the authors open a debate on biogeographical concepts, and present an alternative philosophy for biogeographical research in the context of their recently described biogeographical subregion called ‘Pandora’. We disagree with their approach and conclusions, and comment on several issues related to our differing conceptual approaches for biogeographical research; namely, our use of molecular phylogenetic analyses, including time estimates; and Parenti & Ebach's reliance on taxon/general area cladograms. Finally, we re‐examine their ‘tests’ supporting the existence of ‘Pandora’.     

Molecular phylogeny of an endemic radiation of Cuban toads (Bufonidae: Peltophryne) based on mitochondrial and nuclear genes

Aim In this study we present a molecular phylogenetic and phylogeographical analysis of Peltophryne (Anura: Bufonidae), an endemic genus of Antillean toads, to investigate the spatial and temporal origins of the genus, with particular focus on the eight Cuban species. Location Greater Antilles, with extensive sampling of the Cuban archipelago. Methods We obtained DNA sequence data from two mitochondrial genes, cytochrome c oxidase subunit I (COI) and ribosomal RNA (16S), for 124 toads representing all eight Cuban species, and combined this with published data from Hispaniola (one of three species) and Puerto Rico (one of one species) to establish a molecular phylogeny for Peltophryne. In addition, we explored the phylogeographical structure of widespread Cuban species. For a subset of 42 toads we also obtained DNA sequence data from two nuclear genes, recombination activator‐1 (RAG‐1) and chemokine receptor 4 (CXCR‐4). We combined our molecular data with published DNA sequences from a global sample of bufonid toads to place the spatial and temporal origins of Peltophryne in the Caribbean within a fuller geographical and phylogenetic context. Results All phylogenetic analyses supported the monophyly of West Indian toads. The ancestor of Peltophyrne diverged from its mainland source around the Eocene–Oligocene boundary, with a subsequent radiation across the Caribbean islands taking place during the Miocene. Cuban species are monophyletic with a basal split in the early–middle Miocene that separates extant small‐bodied from large‐bodied species. Extensive mitochondrial DNA (mtDNA) sampling within widespread Cuban species revealed contrasting phylogeographical patterns. Peltophryne taladai and P. empusa showed deeply divergent lineages, whereas no geographical structure was observed in the widespread P. peltocephala. Main conclusions Our timeline for Peltophryne diversification is consistent with a biogeographical model requiring no long‐distance overwater dispersal. Although confidence intervals on divergence time estimates are wide, the stem age of Peltophyrne coincides with the hypothesized GAARlandia landspan or archipelago, which may have connected South America briefly with the Antilles. The ages of Peltophryne for Puerto Rico, Hispaniola and Cuba are consistent with a recently proposed vicariance scenario for the region. Our molecular results support the recognition of all eight species in Cuba, and provide evidence of possible cryptic species.     

Molecular phylogeny of the endemic Philippine rodent Apomys (Muridae) and the dynamics of diversification in an oceanic archipelago

We analysed the phylogenetic relationships of ten of the 13 known species of the genus Apomys using DNA sequences from cytochrome b . Apomys, endemic to oceanic portions of the Philippine archipelago, diversified during the Pliocene as these oceanic islands arose de novo . Several of the speciation events probably took place on Luzon or Mindanao, the two largest, oldest, and most topographically complex islands. Only one speciation event is associated with vicariance due to Pleistocene sea-level fluctuation, and a Pleistocene diversification model in which isolation is driven by sea-level changes is inconsistent with the data. Tectonic vicariance is nearly absent from the Philippines, in which tectonic coalescence plays a significant role. Most speciation events (about two-thirds) are associated with dispersal to newly developed oceanic islands. The data imply that the species have persisted for long periods, measured in millions of years after their origins; further implications therefore are that faunal turnover is very slow, and persistence over geological time spans is more prominent than repeated colonization and extinction. Neither the equilibrium nor the vicariance model of biogeography adequately encompasses these results; a model incorporating colonization, extinction, and speciation is necessary and must incorporate long-term persistence to accommodate our observations.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80 , 699–715.     

Northern Hemisphere origin,transoceanic dispersal,and diversification of Ranunculeae DC. (Ranunculaceae) in the Cenozoic

Aim The role of dispersal versus vicariance for plant distribution patterns has long been disputed. We study the temporal and spatial diversification of Ranunculeae, an almost cosmopolitan tribe comprising 19 genera, to understand the processes that have resulted in the present inter‐continental disjunctions. Location All continents (except Antarctica). Methods Based on phylogenetic analyses of nuclear and chloroplast DNA sequences for 18 genera and 89 species, we develop a temporal–spatial framework for the reconstruction of the biogeographical history of Ranunculeae. To estimate divergence dates, Bayesian uncorrelated rates analyses and four calibration points derived from geological, fossil and external molecular information were applied. Parsimony‐based methods for dispersal–vicariance analysis (diva and Mesquite ) and a maximum likelihood‐based method (Lagrange ) were used for reconstructing ancestral areas. Six areas corresponding to continents were delimited. Results The reconstruction of ancestral areas is congruent in the diva and maximum likelihood‐based analyses for most nodes, but Mesquite reveals equivocal results at deep nodes. Our study suggests a Northern Hemisphere origin for the Ranunculeae in the Eocene and a weakly supported vicariance event between North America and Eurasia. The Eurasian clade diversified between the early Oligocene and the late Miocene, with at least three independent migrations to the Southern Hemisphere. The North American clade diversified in the Miocene and dispersed later to Eurasia, South America and Africa. Main conclusions Ranunculeae diversified between the late Eocene and the late Miocene. During this time period, the main oceanic barriers already existed between continents and thus dispersal is the most likely explanation for the current distribution of the tribe. In the Southern Hemisphere, a vicariance model related to the break‐up of Gondwana is clearly rejected. Dispersals between continents could have occurred via migration over land bridges, such as the Bering Land Bridge, or via long‐distance dispersal.     

Historical biogeography of the coffee family (Rubiaceae,Gentianales) in Madagascar: case studies from the tribes Knoxieae,Naucleeae, Paederieae and Vanguerieae

Aim In Madagascar the family Rubiaceae includes an estimated 650 species representing 95 genera. As many as 98% of the species and 30% of the genera are endemic. Several factors make the Rubiaceae a model system for developing an understanding of the origins of the Malagasy flora. Ancestral area distributions are explicitly reconstructed for four tribes (Knoxieae, Naucleeae, Paederieae and Vanguerieae) with the aim of understanding how many times, and from where, these groups have originated in Madagascar. Location Indian Ocean Basin, with a focus on Madagascar. Methods Bayesian phylogenetic analyses are conducted on the four tribes. The results are used for reconstructing ancestral areas using dispersal–vicariance analyses. Phylogenetic uncertainties in the reconstructions are accounted for by conducting all analyses on the posterior distribution from the analyses. Results Altogether, 11 arrivals in Madagascar (one in Paederieae, five in Knoxieae, three in Vanguerieae, and two in Naucleeae) are reconstructed. The most common pattern is a dispersal event (followed by vicariance) from Eastern Tropical Africa. The Naucleeae and Paederieae in Madagascar differ and originate from Asia. Numerous out‐of‐Madagascar dispersals, mainly in the dioecious Vanguerieae, are reconstructed. Main conclusions The four tribes arrived several times in Madagascar via dispersal events from Eastern Tropical Africa, Southern Africa and Tropical Asia. The presence of monophyletic groups that include a number of species only found in Madagascar indicates that much endemism in the tribes results from speciation events occurring well after their arrival in Madagascar. Madagascar is the source of origin for almost all Rubiaceae found on the neighbouring islands of the Comoros, Mascarenes and Seychelles.     

A tale of North and South America: time and mode of dispersal of the amphitropical genus Munroa (Poaceae,Chloridoideae)

Plant disjunctions have provided some of the most intriguing distribution patterns historically addressed by biogeographers. We evaluated the three hypotheses that have been postulated to explain these patterns [vicariance, stepping‐stone dispersal and long‐distance dispersal (LDD)] using Munroa, an American genus of grasses with six species and a disjunct distribution between the desert regions of North and South America. The ages of clades, cytology, ancestral characters and areas of distribution were investigated in order to establish relationships among species, to determine the time of divergence of the genus and its main lineages, and to understand further the biogeographical and evolutionary history of this genus. Bayesian inference recovered the North American M. pulchella as sister species to the rest. Molecular dating and ancestral area analyses suggest that Munroa originated in North America in the late Miocene–Pliocene (7.2 Mya; 8.2–6.5 Mya). Based on these results, we postulate that two dispersal events modelled the current distribution patterns of Munroa: the first from North to South America (7.2 Mya; 8.2–6.5 Mya) and the second (1.8 Mya; 2–0.8 Mya) from South to North America. Arid conditions of the late Miocene–Pliocene in the Neogene and Quaternary climatic oscillations in North America and South America were probably advantageous for the establishment of populations of Munroa. We did not find any relationship between ploidy and dispersal events, and our ancestral character analyses suggest that shifts associated with dispersal and seedling establishment, such as habit, reproductive system, disarticulation of rachilla, and shape and texture of the glume, have been important in these species reaching new areas. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 110–125.     

Ecological divergence and sexual selection drive sexual size dimorphism in new world pitvipers (Serpentes: Viperidae)

Hypotheses for the origin and maintenance of sexual size dimorphism (SSD) fall into three primary categories: (i) sexual selection on male size, (ii) fecundity selection on female size and (iii) ecological selection for gender‐specific niche divergence. We investigate the impact of these forces on SSD evolution in New World pitvipers (Crotalinae). We constructed a phylogeny from up to eight genes (seven mitochondrial, one nuclear) for 104 species of NW crotalines. We gathered morphological and ecological data for 82 species for comparative analyses. There is a strong signal of sexual selection on male size driving SSD, but less evidence for fecundity selection on female size across lineages. No support was found for allometric scaling of SSD (Rensch's rule), nor for directional selection for increasing male size (the Fairbairn–Preziosi hypothesis) in NW crotalines. Interestingly, arboreal lineages experience higher rates of SSD evolution and a pronounced shift to female‐biased dimorphism. This suggests that fecundity selection on arboreal females exaggerates ecologically mediated dimorphism, whereas sexual selection drives male size in terrestrial lineages. We find that increasing SSD in both directions (male‐ and female‐biased) decreases speciation rates. In NW crotalines, it appears that increasing magnitudes of ecologically mediated SSD reduce rates of speciation, as divergence accumulates within species among sexes, reducing adaptive divergence between populations leading to speciation.     

'First' appearances in the Cenozoic land-mammal record of the Greater Antilles: significance and comparison with South American and Antarctic records

Aim Through analysis of fossil records, the aim of this paper is to show that fossil representatives of at least three land‐mammal clades (pitheciine atelid primates, heteropsomyine echimyid rodents, and megalonychid phyllophagan xenarthrans) that once lived in the Greater Antilles are as old as, if not older than, ‘first’ occurrences of these same groups on the South American mainland. Location Greater Antilles, South America, Antarctic Peninsula. Methods Analysis of Cenozoic land‐mammal fossil records for the three areas. Results Comparison reveals an interesting similarity to the Tertiary vertebrate palaeontological record for the Antarctic Peninsula (Seymour Island), in the sense that the latter also includes early (Eocene) representatives of some typical ‘South American’ groups (e.g. meridiungulates, sloths, certain marsupial groups). Conclusions Given how limited the Antillean and Antarctic records are in quantity and quality, it seems unlikely that these ‘first’ appearances have much bearing on real origins (basal divergences). Rather, it suggests that the fossil basis for interpreting the origin and earliest diversification of ‘South American’ clades during the latest Cretaceous/early Cenozoic is probably even scantier than generally realized. In particular, the Antillean record strengthens arguments that some crown‐group continental lineages are considerably older than fossil evidence currently allows – a point increasingly (if unevenly) supported by molecular studies of many of the same clades.     

The Hawaiian Archipelago is a stepping stone for dispersal in the Pacific: an example from the plant genus Melicope (Rutaceae)

Aim Pacific biogeographical patterns in the widespread plant genus Melicope J.R. Forst. & G. Forst. (Rutaceae) were examined by generating phylogenetic hypotheses based on chloroplast and nuclear ribosomal sequence data. The aims of the study were to identify the number of colonization events of Melicope to the Hawaiian Islands and to reveal the relationship of Hawaiian Melicope to the Hawaiian endemic genus Platydesma H. Mann. The ultimate goal was to determine if the Hawaiian Islands served as a source area for the colonization of Polynesia. Location Nineteen accessions were sampled in this study, namely eight Melicope species from the Hawaiian Islands, four from the Marquesas Islands, one species each from Tahiti, Australia and Lord Howe Island, two Australian outgroups and two species of the Hawaiian endemic genus Platydesma. To place our results in a broader context, 19 sequences obtained from GenBank were included in an additional analysis, including samples from Australia, Papua New Guinea, New Zealand, Southeast Polynesia and Asia. Methods DNA sequences were generated across 19 accessions for one nuclear ribosomal and three chloroplast gene regions. Maximum parsimony analyses were conducted on separate and combined data sets, and a maximum likelihood analysis was conducted on the combined nuclear ribosomal and chloroplast data set. A broader nuclear ribosomal maximum parsimony analysis using sequences obtained from GenBank was also performed. Geographic areas were mapped onto the combined chloroplast and nuclear ribosomal tree, as well as onto the broader tree, using the parsimony criterion to determine the dispersal patterns. Results Phylogenetic analyses revealed that Platydesma is nested within Melicope and is sister to the Hawaiian members of Melicope. The Hawaiian Melicope + Platydesma lineage was a result of a single colonization event, probably from the Austral region. Finally, Marquesan Melicope descended from at least one, and possibly two, colonization events from the Hawaiian Islands. Main conclusions These data demonstrate a shifting paradigm of Pacific oceanic island biogeography, in which the patterns of long‐distance dispersal and colonization in the Pacific are more dynamic than previously thought, and suggest that the Hawaiian Islands may act as a stepping stone for dispersal throughout the Pacific.     

Phylogeny and divergence time of island tiger beetles of the genus Cylindera (Coleoptera: Cicindelidae) in East Asia

To examine the diverse colonization histories in eight tiger beetle species of the genus Cylindera (Coleoptera: Cicindelidae) on the East Asian islands, we conducted phylogenetic analyses and divergence time estimation using mitochondrial cytochome oxidase subunit I (COI) and nuclear 28S rDNA sequences. The island fauna consisted of four subgenera: Apterodela, Cicindina, Ifasina, and Cylindera. Apterodela is a flightless group with large bodies, whereas the others are fliers with small bodies. In Apterodela, the divergence among endemic species in Taiwan, Japan, and the mainland was ancient (2.1–4.7 Mya), as expected from their flightlessness. Their dispersal might have occurred across the extended landmass in East Asia during the Pliocene. In the subgenus Cicindina, Cylindera elisae has spread throughout East Asia, from which an endemic species, Cylindera bonina, was derived on the oceanic Bonin Islands during the early Pleistocene (0.9 Mya). This indicates the significance of Cylindera bonina, which is currently confined to a single island, for conservation. In the subgenus Ifasina, Cylindera kaleea is widely distributed in East Asia, and its sister species Cylindera humerula, endemic to Okinawa Island, diverged 1.0 Mya, whereas Cylindera psilica on Taiwan and the Yaeyama Islands diverged approximately 0.8 Mya. In the subgenus Cylindera, the colonization of Cylindera gracilis in Japan from the mainland occurred during the last glacial period. With the exception of C. bonina, which likely colonized new territories by flight or drifting, other dispersal events might have used land connections that occurred repeatedly during the Pliocene and Pleistocene. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 715–727.     

Deep intra‐island divergence of a montane forest endemic: phylogeography of the Puerto Rican frog Eleutherodactylus portoricensis (Anura: Eleutherodactylidae)

Aim Hypotheses proposed for lineage diversification of tropical montane species have rarely been tested within oceanic islands. Our goal was to understand how basin barriers and Pleistocene climatic fluctuations shaped the distribution of diversity in Eleutherodactylus portoricensis (Eleutherodactylidae), a frog endemic to the montane rain forests of Puerto Rico. Location The north‐eastern (Luquillo) and south‐eastern (Cayey) mountains of Puerto Rico. Methods We generated mitochondrial DNA (mtDNA) control region sequences (c. 565 bp) from 144 individuals of E. portoricensis representing 16 localities, and sequenced 646 bp of cytochrome b and 596 bp of nuclear DNA (nDNA) rhodopsin exon and intron 1 from a subset of individuals. We conducted a phylogenetic analysis on the mtDNA sequence data and explored population substructure with maximum parsimony networks, a spatial analysis of molecular variance, and pairwise F_ST analysis. Coalescent simulations were performed to test alternative models of population divergence in response to late Pleistocene interglacial periods. Historical demography was assessed through coalescent analyses and Bayesian skyline plots. Results We found: (1) two highly divergent groups associated with the disjunct Luquillo and Cayey Mountains, respectively; (2) a shallow mtDNA genetic discontinuity across the La Plata Basin within the Cayey Mountains; (3) phylogeographic congruence between nDNA and mtDNA markers; (4) divergence dates for both mtDNA and nDNA pre‐dating the Holocene interglacial (c. 10 ka), and nDNA suggesting divergence in the penultimate interglacial (c. 245 ka); and (5) historical demographic stability in both lineages. Main conclusions The low‐elevation Caguas Basin is a long‐term barrier to gene flow between the two montane frog populations. Measures of genetic diversity for mtDNA were similar in both lineages, but lower nDNA diversity in the Luquillo Mountains lineage suggests infrequent dispersal between the two mountain ranges and colonization by a low‐diversity founder population. Population divergence began prior to the Holocene interglacial. Stable population sizes over time indicate a lack of demonstrable demographic response to climatic changes during the last glacial period. This study highlights the importance of topographic complexity in promoting within‐island vicariant speciation in the Greater Antilles, and indicates long‐term persistence and lineage diversification despite late Pleistocene climatic oscillations.