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A comprehensive overview of the genetic diversity in Thylamys elegans (Didelphimorphia: Didelphidae): establishing the phylogeographic determinants

Revista Chilena de Historia Natural volume 94, Article number: 5 (2021) Cite this article

Abstract

Background

For the genus Thylamys, the rivers have been reported as barriers to dispersal, limiting current and historical distribution of its lineages. We hypothesized that the Maipo river has affected the genetic structure of northern and southern lineages of Thylamys elegans, recovering a phylogenetic relationships with reciprocally monophyletic sister groups on opposite river banks. We evaluated the role of other rivers in the Mediterranean zone of Chile as historical and recent modulators of the biogeographic processes of this species.

Methods

We applied a phylogeographic approach, using the cytochrome-b mitochondrial gene for 93 individuals of T. elegans, from 37 localities in a latitudinal gradient between 21°25’ and 35˚56’S, encompassing a geographic area between the Atacama Desert and most of the Mediterranean Chilean zone.

Results

The phylogenetics results recovered six lineages within T. elegans: Thylamys elegans elegans, Thylamys elegans coquimbensis, the Loa lineage and three other lineages not described previously (Aconcagua, South 1 and South 2). We suggest that following rivers play a role like primary barrier: the Maipo river in the genetic differentiation of northern and southern ancestral lineages, and the Mataquito river and its tributary Teno river for the South 1 and South 2 lineages. On the other hand, the Quilimarí river preserve the genetic divergence in T. e. coquimbensis and Aconcagua lineage and the Aconcagua river in Aconcagua lineage and T. e. elegans acting like secondary barriers.

Conclusions

We concluded that the genetic diversity and biogeographic history of T. elegans was shaped by mountain glaciers, changes in river water levels during the Pleistocene glaciations and hyperaridity, promoting the differentiation and persistance of the T. elegans lineages.

Background

Since the 19th century, rivers have been proposed as geographical barriers to dispersal for several taxa [1]. The riverine barrier hypothesis proposes that populations of different river banks become progressively isolated each other and predicts populations of opposite banks with reciprocally monophyletic relationships [2, 3]. The effects of rivers on the biota has become more evident by the use of molecular and bioinformatics tools. Three hypotheses are proposed to explain riverine divergence by mean of primary differentiation, secondary contact and dispersal: (1) primary differentiation, with a river acting as a complete vicariant barrier for an existing taxon range, resulting in a topology with reciprocally monophyly of sister clades from opposite banks; (2) secondary differentiation, with a river as a common contact zone acting as a barrier to dispersal, preventing secondary contact of previously differentiated populations and a topology with opposite river lineages showing more recent common ancestor with others populations of the same river bank and lineages from opposite banks are not sister clades; (3) dispersal events from an established populations to the opposite riverbank, with the river being a permeable barrier to gene flow and a topology with paraphyly [2,3,4]. If rivers represent a barrier to populations of some species, it is expected that the diversification between populations from opposite riverbanks coincide with the formation of the river. If they do not coincide temporarily, the river is unlikely to be the primary divergence agent, but then it could have acted as a barrier to gene flow [5].

Didelphidae is one of the oldest families of extant mammal [6]. Species of this family inhabit in forest and open habitat in the Neotropics [7]. Rivers have been reported as geographic range boundaries or as barriers to gene flow in some populations of didelphid marsupials of genus Philander, Marmosa, Gracilinanus, Marmosops and Cryptonanus in the Amazon River [8,9,10]; the Paraná and Paraguay rivers [11, 12], the São Francisco river [13, 14] the Paraguay river [15], the Tocantins river [14], the Doce and Paraíba do Sol rivers [16] and Tapajós rivers [10]. In Thylamys, the effect of rivers such as geographic barrier to gene flow or geographic boundary of distributional range has been reported for the following rivers: Paraná for T. citellus and T. pulchellus; Bermejo for T. pulchellus and T. pusillus, Paraguay for T. pusillus, Paraná and Uruguay for T. citellus [17], Pilcomayo for T. pusillus A and T. pusillus B; and Paraná and Uruguay for T. pusillus C [18]. Paraná for T. pusillus C and T. pusillus A, and Paraguay for T. pusillus B, T. pusillus C and T. pusillus A [18], and Cañete for T. tatei and T. sp [19].

Thylamys elegans is one out of two Thylamys species present in Chile [19, 20]. This species has a huge distribution from the north of the Loa river Mouth (21°25’S) to Angol and adjacent areas of the Nahuelbuta coastal range (37°50’S) according to historical records, covering an extension close to 1850 km [19,20,21,22]. Thylamys elegans  is a mouse-like marsupial whose activity is mainly arboreal and crepuscular. Its diet items are composed mainly by insects although fruits, small vertebrates and even carrion occasionally are consumed [7, 23]. This and other species of Thylamys genus are characterized by its tail incrassation during winter periods when the specimens fall in torpor [23,24,25]. A marked north-south climatic gradient is present in this wide distribution, with different environment in each geographical zone [26,27,28]. Thus, those populations that inhabit xeric environments are associated with small patches of available vegetation (see Fig. 1b), while the specimens that inhabit in humid environment had several different habitats available even into brushy ecotones of relictual cloud forest of the Coquimbo region, northern and central part of the Coastal ranges and the steppes of Central Chile [19, 20, 23, 29, 30] (See Fig. 1c). Clearly this huge and contrast distribution produce a strong cline in size, color and shape of the different populations [20, 21, 23, 24, 31, 32]. Actually, the differences between clines have been enough to suggest three subspecies based only in morphological characters [21, 23, 24, 32], but its distribution boundaries are still uncertain [19, 20, 33].

Fig. 1
figure 1

Morphological variability and environment of Thylamys elegans. a Adult specimen and landscape from the Loa river Mouth, Loa lineage (Clade A); b Adult specimen corresponding to T. e. coquimbensis from Paihuano and ravine from Llanos de Challe (Clade B); c Adult specimen and landscape from Los Molles corresponding to the Aconcagua lineage (Clade C); d Adult specimen corresponding to T. e. elegans from Punta Curaumilla and landscape from Las Docas (Clade D; e) Adult specimen from Lipimávida and landscape from Pupuya, corresponding to the South 1 lineage (Clade E); f Adult specimen (not sequenced) and landscape from Nahuelbuta Coastal range, probably corresponding to the South 2 lineage (Clade F). Northern clade encompasses the Loa, T. e. coquimbensis, Aconcagua and T. e. elegans lineages and southern clade encompasses the South 1 and South 2 lineages

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Additionally, studies have found genetic structure in the distribution of T. elegans [19, 20, 34], but the genetic clades not match with the morphological subspecies described (see [20, 33] for T. e. coquimbensis). These evidences suggest that morphological variability could be more related with the environment than the genetic fingerprint and for that reason is still difficult delimit the distributional range of the different lineages or subspecies. Anyway, so far, what is limiting the distribution of each lineage or subspecies in T. elegans is still uncertain. A previous study proposed in Mediterranean zone of Chile, the Maipo river as an strong geographic barrier in the genetic differentiation of northern and southern clades of Thylamys elegans [19] and a genetic differentiation congruent with the position of the Maipo river has been reported for other taxa [35,36,37,38,39,40,41]. Indeed, some rivers can act as barriers to gene flow and/or geographic boundary of distribution structuring genetic diversity in different taxa from Chile [36, 41,42,43,44,45,46]. However, none of these papers discussed in detail if the riverine divergence would be a primary or secondary differentiation [47]. On the other hand, the historical and recent effects of other rivers different to Maipo river on the differentiation of T. elegans lineages are still unknown, being necessary to evaluate if the role of rivers was for primary diversification, secondary contact or dispersal [4]. Knowing these effects is very relevant in the geographical context in which this species is distributed, where the spatial complexity of the landscape is proposed as the cause of the high endemism of one of South America’s biodiversity hotspots [48, 49]. Therefore, under these evidences the hypothesis about the rivers as phylogeographic determinant is novel to test it in T. elegans given that in Chile a role of rivers in the genetic differentiation of a mammal has never been discussed in detail.

Although the largest rivers in South America are in tropical and subtropical regions, the effects of smaller rivers in the temperate region as geographic boundaries or barriers to gene flow were reported in Chile for the Huasco, Copiapó, Elqui, Aconcagua, Maipo, Mataquito, Claro, Lircay, Maule, Itata and Bío-Bío rivers [35,36,37,38,39,40,41,42,43,44,45,46, 50,51,52,53,54,55]. Therefore, the main goal of this study was to evaluate, through a phylogeographic approach, the role of some rivers of Mediterranean Chilean zone on the genetic structure of T. elegans. We propose that some riverine barriers from Mediterranean zone of Chile shape the genetic diversity of Thylamys elegans, triggering the genetic divergence of its lineages through vicariant events as primary riverine divergence, or persistence of its genetic differentiation with rivers acting as geographic boundaries of lineages previously differentiated and posterior secondary riverine differentiation.

Methods

Collections

We perform nine field campaigns between 2010 and 2012 which covered most of the distributional range of T. elegans. From these campaigns and voucher specimens stored at the Colección de Flora y Fauna Patricio Sánchez Reyes, Pontificia Universidad Católica de Chile, we had available samples from north of the Loa river Mouth, (21°25’S) in the Tarapacá region to Tregualemu (35°56’S) in the Maule region (Fig. 2, see details in Additional file 1: Appendix I). Specimens were collected with Sherman traps (8 × 9 × 23 cm) using a mixture of oat, banana and canned fish as bait or crushed oat. Captured individuals were euthanized with isofluorane overdose and cervical dislocation. Collection and handling recommendations were followed according to the American Society of Mammalogists [56]. Samples were obtained from different tissues such as blood, hair or liver. Also from ear skin or tail from corpses found on fieldwork and donations of tissues by collaborators. Eighteen samples correspond to donations, 63 samples belonged to Colección de Flora y Fauna Patricio Sánchez Reyes, Pontificia Universidad Católica de Chile and 14 samples from 10 localities were captured and euthanized in this study (See details in Additional file 1: Appendix I). The samples were stored in cryotubes preserved in liquid nitrogen or 70 % ethanol. All voucher specimens (tissues, skins or skeletons) were stored at the Colección de Flora y Fauna Patricio Sánchez Reyes, Pontificia Universidad Católica de Chile.

Fig. 2
figure 2

Summarized phylogeny and map with the 37 sampled spots in this study. The colors of the sampled spots match with clades on the tree (also for Fig. S1 and Fig. S2). Most important branches of the rivers that limit the lineages of T. elegans are shown (Quilimarí, Aconcagua, Maipo, Mataquito and its tributary Teno). Loa lineage (Clade A: blue); T. e. coquimbensis (Clade B: cyan); Aconcagua lineage (Clade C: orange); T. e. elegans (Clade D: brown); South 1 lineage (Clade E: green); South 2 lineage (Clade F: red). Northern clade encompasses the Loa, T. e. coquimbensis, Aconcagua, and T. e. elegans lineages and southern clade encompasses the South 1 and South 2 lineages

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DNA extraction, amplification and sequencing

DNA was extracted with phenol-chloroform procedures [57]. The complete cyt-b mitochondrial gene (1149 base pairs) was used for 93 individuals of T. elegans from 37 localities and 2 sequences corresponding to T. pallidior A and T. pallidior B respectively as outgroup, (including 32 sequences from previous studies in Thylamys genus [19, 20, 58] and 63 new sequences generated in this study with the following genbank access number (MZ868645- MZ868707, see details in Additional file 1: Appendix I). This gene has been widely used in phylogeographic studies in Thylamys genus because its variability [17, 20, 33, 58]. PCR amplification reactions followed described protocols [19, 20], and products were purified with QIAquick PCR Purification Kit (QUIAGENTM Inc., Valencia, CA, USA), and sequenced in MACROGEN Inc. (Seoul, Korea). Sequences were edited in Bioedit [59] and aligned in Clustal W [60] using default parameters and encoded to aminoacid in DnaSP v6 [61] to verify the lack of internal stop codons.

Phylogenetic reconstruction

The phylogenetic reconstructions was based on 49 haplotypes and 95 sequences using Maximum Likelihood (ML) criterion on the online version of IQ-TREE software [62] available at http://iqtree.cibiv.univie.ac.at [63]. The best model of evolution was retrieved with ModelFinder [64] implemented in IQ-TREE using the Bayesian Information Criterion (BIC) prior to the construction of the ML trees. To assess branch support, the ultrafast bootstrap approximation (UFboot2) with 1000 replicates was implemented [65]. Bayesian Inference (IB) was performed using Mr. Bayes 3.2.6 [66]. Four simultaneous Markov chain Monte Carlo chains were run for 10,000,000 generations, with a sampling frequency of 1,000 generations. The first 25 % trees were discarded as burn-in and remaining trees were used to compute a 50 % majority rule consensus tree and to obtain posterior probability estimates for each clade. The ML and BI phylogenies were rooted using T. pallidior A and T. pallidior B as outgroup (see details in Additional file 1: Appendix I, Fig S1, Fig S2) following to [19, 58]. To assess the genetic distance between lineages within T. elegans a corrected distance Kimura 2-parameters (K2P) was calculated in MEGA 7.0 [67].

Genetic structure

To estimate the geographic population structure of T. elegans in a Bayesian framework, we used GENELAND v4.0 [68]. The number of genetic clusters (K) was determined using a prior of K between 1 and 37 (number of localities used in this study). We performed 10 independent runs of 5,000,000 iterations, sampling every 1,000 steps. Burning and convergence of the chains were determined with a 0.1 cutoff value and using uncorrelated and correlated frequency models, selecting the most probable model by using the Bayes Factor statistic [69]. Correlated frequency model was chosen and we set the K value to 6 considering the posterior probability distribution of the parameter. After that, five runs were post-processed by burning 5 % of first iterations and we obtain the posterior probability of assignment for each individual to a genetic cluster and to each pixel in the spatial domain. Maximum number of Poisson-Voronoi tessellation nuclei was set at 279 according to the number of genotypes used for the analysis (93 × 3) [70].

Divergence times

To estimate the divergence times for the T. elegans lineages, we used the Bayesian algorithm implemented in BEAST 2.5.2 [71]. The best molecular clock model was selected by Bayes Factor comparing three clock models (strict, uncorrelated lognormal relaxed and uncorrelated exponential relaxed) in Tracer v1.5 [72]. The uncorrelated lognormal relaxed molecular was chosen, using as priors the general time reversible model of sequence evolution (GTR + G) and a Yule speciation process. The calibration points selected for the analysis following to [19]were the same T. pallidior-T. elegans molecular divergence, estimated at 6.11 Million year ago (Mya), (Highest posterior density HPD: 5.92-6.3), and the T. tatei-T. sp molecular divergence at 4.65 Mya (HPD: 4.46-4.85) (Fig S3). Estimate of posterior distribution was obtained through Markov Chain Monte Carlo MCMC method with 20,000,000 iterations, sampling parameters every 10,000th steps, and burning the first 10,000 to achieve convergence of posterior probability distribution. The convergence of samples obtained by MCMC method was visualized in Tracer v1.5 [72]. We verified if the Effective Sample Size of all parameters had values greater than 200. Maximum credibility tree was calculated in TreeAnotator v1.7.0 [73]. The tree was displayed and edited in Figtree 1.4.2 [74].

Results

BIC identified the HKY+F+G4 model as the best nucleotide substitution model for a matrix with 49 haplotypes and other with 95 sequences. Gamma shape distribution parameter was 0.2818 for haplotype matrix and 0.183 for sequences matrix. Both ML and IB reconstruction with haplotypes and all sequences showed the same phylogenetic relationship among six lineages (see Fig. 2, Fig. S1 and Fig. S2). T. elegans is a clade highly supported (100/1). The ingroup exhibited six monophyletic groups with high bootstrap supports and posterior probability values (Fig. S1 and Fig. S2). The southern clade contained the South 1 and South 2 lineages (99/1), and the northen clade contained T. e. elegans sister to (T. e. coquimbensis, (Loa lineage, Aconcagua lineage)) with high support (97/1). The Loa lineage (Clade A) is restricted to north of the Loa river mouth (21°25’S) (1 locality, n = 6). The Aconcagua lineage (Clade C) encompasses localities from Fundo el Roble (32°16’S) to Fundo Chuico Blanco (32°48’S) covered about 100 km from the Quilimarí river and the Santa Inés-Imán mountain range to the Aconcagua river and the Chacabuco range (7 localities, n = 15). T. e. coquimbensis (Clade B) encompasses localities from Quebrada El León (26°57’S) to Valle El Mauro (31°58’S). The southern boundary would be the Quilimarí river and Santa Ines-Imán mountain range (8 localities, n = 19). On the other hand, T. e. elegans (Clade D), encompasses localities from La Campana (32°57’S) to Viña Leyda (33°34’S) between the Aconcagua river and Chacabuco range and the Maipo river and Altos de Cantillana range (10 localities, n = 33). The South 1 lineage (Clade E) encompasses localities from San Enrique (33°53’S) to Duao (34°52’S), between the Maipo to Mataquito river and its tributary Teno river (7 localities, n = 13). The South 2 lineage (Clade F) encompasses localities from Los Queñes (35°0’S) to Tregualemu (35°56’S), between the Mataquito and Teno rivers to Tregualemu (4 localities, n = 7) (Fig. S1, Fig. S2).

The corrected distance (K2P) values were between 2 % for the South 1 and South 2 lineages to 11.9 % for the Loa and South 1 lineages (Table 1). On the other hand, our results show a genetic distance of 5.5 % between the northern clade (i.e. Loa lineage, T. e. coquimbensis. Aconcagua lineage and T. e. elegans) and southern clade (i.e. South 1 lineage and South 2 lineage).

Table 1 Corrected genetic distance values between the six lineages of T. elegans using the K2P model
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GENELAND analysis detected six genetic clusters (Fig. 3) which fit with the six lineages of T. elegans recovered in the phylogenetics reconstruction (Fig. 2, Fig. S1 and Fig. S2). Detection of the geographical genetic discontinuities correspond to the Loa, Quilimarí, Aconcagua, Maipo, Mataquito and Teno rivers and the Santa Inés-Imán, Chacabuco and Altos de Cantillana mountain ranges previously described (Figs. 2 and 3). GENELAND (Fig. 3) estimated clusters corresponding to the following lineages described in Fig. 2, Fig. S1 and Fig. S2: (1) Loa (Clade A); (2) T. e. coquimbensis (Clade B); (3) Aconcagua (Clade C); (4) T. e. elegans (Clade D); (5) South 1 (Clade E), and (6) South 2 (Clade F). T. e. coquimbensis encompass 550 km, and the Aconcagua, T. e. elegans, South 1 and South 2 lineages together encompass 365 km (Fig. 3).

Fig. 3
figure 3

Genetic structure in geographic space of T. elegans. Maps of posterior probabilities isoclines of genetic clusters membership with its respective populations belonging to a panmictic unit correspond to the six lineages of T. elegans detected by GENELAND analyses. Last column: synthetic map of the K-origin of each pixel. Blue line is the Maipo river such a geographic boundary between the northern and southern clades; other six columns: relative posterior probability of belonging to each K cluster. Black dots show sampled populations and lighter background colours indicate higher posterior probability of membership to the given K cluster. Thinner black lines are isoclines of inclusion probability and numbers are posterior probabilities values. Cluster 1 correspond to Loa lineage (Clade A), Cluster 2 correspond to T. e. coquimbensis (Clade B), Cluster 3 correspond to Aconcagua lineage (Clade C), Cluster 4 correspond to T. e. elegans (Clade D), Cluster 5 correspond to South 1 lineage (Clade E), and Cluster 6 correspond to South 2 lineage (Clade F). Northern clade encompasses the Loa, T. e. coquimbensis, Aconcagua and T. e. elegans lineages and southern clade encompasses the South 1 and South 2 lineages

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The T. elegans clades diverged as follow (see Fig. 4 and Fig. S3): northern and southern clades, 3.14 Mya (HPD: 2.95-3.33); T. e. elegans from the clade with T. e. coquimbensis sister to the Loa and Aconcagua lineages, 1.84 Mya (HPD: 1.41-2.27); T. e. coquimbensis from the Loa and Aconcagua lineages, 1.41 Mya (HPD: 1.07-1.8); the Loa and Aconcagua lineages, 1.28 Mya (HPD: 0.91-1.64); the South 1 and South 2 lineages, 0.81 Mya (HPD: 0.48-1.2) (Fig. 4); the Andean-Coastal clade from T. pallidior A and T. pallidior B, 3.35 Mya (HPD: 3.16-3.54), T. sp and T. tatei, 4.65 Mya (HPD: 4.46-4.85) and T. pallidior-T. elegans from T. tatei-T. sp, 7.64 Mya (HPD: 6.61-8.73) (Fig. S3).

Fig. 4
figure 4

Divergence times of the six lineages of T. elegans. Clades correspond to Fig. 2. Number of nodes are average values and bars in yellow are the 95 % HPD. A time scale show the geological ages. Gray shaded areas represent the GPG (~1.68-1.016 Mya) and the CPG (~0.7-0.6 Mya). Below the tree glacial-interglacial cycles were reconstructed using the data available from [82] and the historical ocean temperature available from [84]

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Discussion

Geographical distribution of Clades

We recovered four groups at the north of the Maipo river (southern clade): (1) The Loa lineage, (2) T. e. coquimbensis, (3) T. e. elegans and (4) the new lineage Aconcagua. The Loa lineage (Clade A) is located north of the Loa river mouth (21°25’S), and so far is the only population known for this lineage, but specimens have been recorded in Paposo-Taltal [30] which could belong to this lineage as well. Whereas T. e. coquimbensis (Clade B) has the widest distributional range. Our results extend its distributional range between the coast of Atacama southward to the Coquimbo region from Quebrada El León (26°57’S) to Valle El Mauro (31°58’S), with the Quilimarí river and Santa Inés-Imán mountain range as southern boundary (Figs. 2 and 3, Fig. S1 and Fig. S2). These two lineages inhabits in the hyperarid Atacama in localities as the northern Loa river mouth, Quebrada El León and Llanos del Challe where the rain barely reaches the 10 to 20 mm/yr [75, 76] and are the most extremophilous lineage which inhabit in small patches, strongly associated to rivers, ravines, or riverbeds taking advantage of the available water and the small bushes present there (see Fig. 1a, b).

On the other hand, Our results showed that in the next southern clades the ranges of distribution are drastically reduced. The new lineage Aconcagua (Clade C) is restricted from Fundo El Roble (32°16’S) to Fundo Chuico Blanco (32°48’S), between the Quilimarí river-Santa Inés-Imán mountain range to the Aconcagua river and the Chacabuco mountain range. Same than T. e. elegans (Clade D) which is restricted between the Aconcagua river and Chacabuco range (32°57’S) and the Maipo river and Altos de Cantillana range (33°34’S). At the South of the Maipo river (southern clade), two lineages previously not described were recovered. The South 1 lineage (Clade E) between the Maipo river and Altos de Cantillana range (33°3’S) and the Mataquito river (35°3’S) and its tributary Teno river (34°55’S). Finally, the South 2 lineage (Clade F), restricted at south of the Mataquito-Teno rivers at least until Tregualemu (35°56’S). Interestingly, the specimens from the South 2 lineage could be assigned to T. e. soricinus according to [29], who describe its distribution until Radal Siete Tazas and the junction of the Claro and Maule rivers, which is totally consistent with the distribution of the South 2 lineage (Figs. 2 and 3, Fig. S1 and Fig. S2). Historical records [21, 22, 32] propose that T. e. soricinus could inhabit as far as the south of the Bío-Bío river until Angol and adjacent areas of the Nahuelbuta Coastal range 37°50’S (see Fig. 1f).

In the northern part of the Mediterranean region (31°–35°S), thorny scrublands alternate with sclerophyllous woodlands and relict populations of the Chilean palm, in the Valparaíso region, while in the southernmost zone (36°–38°S), sclerophyllous forests mixed with broadleaf evergreen and deciduous forests form a diverse ecotone in the Mediterranean-temperate climatic transition [26]. In summary, from the landscape point of view, we can divide the distribution of T. elegans lineages in three climatic zones adapted from [26,27,28]: (1) Desert characterized by scarce or null vegetation where inhabit mainly the clades A in Tarapacá region and northern part of clade B in Atacama region, (2) Dry Mediterranean with vegetation type such as dry xerophytic thorn scrublands and evergreen sclerophyllous communities where inhabit mainly the clades C, D and E, but also the southern populations of clade B in Coquimbo region and 3) Wet Mediterranean, dominated by deciduous forest were inhabiting the clade F in Maule region.

Phylogeographic determinants

About 3.5 Mya a dramatic climatic change occurred because was the end of the warm Pliocene as result of global cooling. During this major climate cooling, important glaciations in all Andes occurred [77, 78] and consequently the rivers formation post-Pliocene glaciation [79, 80]. Following further cooling towards the Quaternary and throughout the Quaternary established the South American Arid Diagonal [81] which change the landscape of the continent as is known today. Likely, all these climatic events triggered the separation of the northern and southern Maipo clades by a vicariant event, because the Maipo river flow increase posterior to a glaciation and cooling periods due to melting of glaciers. These geographic barriers could be reinforced for the transversal range that joined the Andes with the Coastal Cantillana range, the Maipo river has been a hard barrier from this period. The reciprocally monophyletic clades in opposite banks and the oldest divergence time (3.14 Mya) are strongly supporting the primary vicariant event as hypothesis of diversification on the Pleistocene (Figs. 2 and 4, Fig. S1, Fig. S2 and Fig. S3). After a huge gap of diversification, around 1.8 Mya stands for the most fundamental change in global climate and climate variability in the Quaternary, referred to as the Mid Pleistocene Transition [82,83,84]. This period coincides with the significant emergence of diversification events in T. elegans at ~1.8-0.8 Mya. During this period, the previous dominant periodicity of climate cycles changed from a 41 kyr to a 100 kyr cycle, causing high amplitude climate oscillations (e.g.[82, 85]). Pronounced cold and warm cycles during the remaining Quaternary most likely caused the repeated cyclical opening and closing of migration corridors, in this case by rivers or hyperaridity, promoting further differentiation in the lineages of T. elegans. These divergence time match with the deep effect that the Great Patagonian Glaciation (GPG~ 1.68-1.016 Mya) generated on a wide range of taxa in southern South America [86]. Therefore, glacial-interglacial cycles of the Quaternary could affect the river water levels fluctuations of the Mediterranean Chilean zone, becoming potential barriers to gene flow of the lineages of T. elegans during melting of glaciers and more permeable barriers during glaciations[35, 36, 40, 55, 87, 88]. During glacial- interglacial cycles, great ice masses descending to around 1100-1300 masl between 33-34°S in the Aconcagua and Maipo valleys [89,90,91]. Around ∼1.84 Mya, the T. e. elegans lineage was separated from the northern lineages because the Aconcagua river and Chacabuco range acted as effective geographic barriers and biogeographical determinants to keep its ancestral range. While the other lineages of T. elegans differed in central and northern Chile in a relatively short period of time. Around ∼1.41 Mya, the lineage T. e. coquimbensis occupied northern areas probably because a hyperarid period between 2 and 1 Mya affected the Atacama Desert region [92], allowing that a small population crossed the Quilimarí river though the coast because the lower river water levels in middle courses and river mouths of the Mediterranean Chilean zone were more permeable barriers [93].

Then, the peripherical differentiation in the Coquimbean Andes avoiding the hyperaridity of the desert, facilitated that this lineage reach its northernmost distribution along the coast in Quebrada el León in posterior favorable conditions. Today the Quilimarí river and the Santa Inés-Imán mountain range seem to be the southern distribution boundary of T. e. coquimbensis but it is not clear if they are strong barriers to southern dispersion allowing secondary divergence. Finally, one of the most complex scenarios occurred about 1.28 Mya, where Central Chile was colonized. Some populations from the Atacama Desert at the north of the Loa river mouth, differentiated into the Loa lineage. Likely, the Loa lineage had a distribution extended further south in the Atacama Desert. Then, the populations were connected by old corridors and perhaps the southernmost dispersal to Central Chile. Huge corridors in the Atacama Desert have been proposed for other organism to explain this strange vicariant distribution with a huge gap [94, 95]. However, these corridor are not permanent and probably have been severely closed during hyperarid periods (as it is now) in the Atacama and today the biota can survive in small pocket with suitable conditions [94], while other middle population were extinguished. The Aconcagua lineage finally differentiated between the Quilimarí river and Santa Inés-Imán mountain range and the Aconcagua river and the Chacabuco range as barrier to southern dispersion allowing secondary divergence. Probably, these events are related, occurring almost at the same period.

On the other hand, the southern history is more recent and simpler, because the phylogeny recovered reciprocally monophyletic groups on opposite banks suggesting that around 0.81 Mya during the Pleistocene, a vicariant event promoted by the Mataquito river and its tributary Teno river caused the divergence between the South 1 and South 2 lineages (Figs. 2 and 4, Fig. S1, Fig. S2 and Fig. S3). Chile was strongly affected by the Pleistocene glaciation, particularly in the south part of the country with an event as the Great Patagonian Glaciation (GPG~1.68-1.016 Mya) and the Coldest Pleistocene Glaciation (CPG~0.7-0.6 Mya). These glaciations could be related with the water levels increase of the Mataquito and Teno rivers [96] and acting such as primary vicariant barrier between both lineage. Mataquito river has been reported as a phylogeographic break at 35° S for terrestrial animals [38, 42].

In general, we have two spatially contrasting scenarios for explain the structure found. Central Chile understanding as the region from the Quilimarí river (32°6’S) to the Bío-Bío river (36°48’S) had a greater influence of glaciations, generating a greater water levels in the past for rivers [35, 36, 40, 55, 87, 88] and these rivers have strongly influenced on the genetic structure of T. elegans, but with different intensity. Thus, Maipo and Mataquito-Teno rivers acted such as primary and strong barriers, while rivers north to Maipo such as Quilimarí and Aconcagua are secondaries barrier which in some parts of their history were permeable for the fauna. On this way, the past climate changes to the hyperaridity would be the key to explain the current distributional range of the T. elegans lineages in the Atacama Desert and northern Mediterranean zone of Chile (i.e. north of the Quilimarí river). The Loa lineage which is enclosed in a small pocket in the north Loa river mouth is currently distributed far of its sister clade (Aconcagua lineage) in Central Chile and is the good example of the dramatic effect of the aridity for the biota, probably extinguishing populations between the Loa and Aconcagua lineages (Fig. 2, Fig. S1 and Fig. S2). However, T. e. coquimbesis would have recently replaced whose anteriorly extinguished populations from Coquimbean Andes. The huge distribution of T. e. coquimbesis in the Atacama desert (Figs. 2 and 3), without genetic structure seem indicate that the effects of rivers are apparently null there, even when some rivers have been reported as important barrier for animals, particularly the Huasco and Copiapó rivers [51, 55]. However, the survivor Atacama populations today are living in small patches with vegetation which are small island in the hyperarid Atacama.

Probably with the creation of the Arid Diagonal and the periodic climate oscillation which changed the landscape several times in the last 1.5 Mya, the different ancestors of each lineage were adapted to xeric environment (clades A and northern part of clade B), mesic (clades C, D,E and southern part of clade B) or humid environment (Clade F) favoring even more the differentiation not drove by barriers. A similar scenario was reported in Abrothrix longipilis with lineages restricted to different bioclimate [26, 47]. Therefore, although today some rivers as the Quilimarí or even the Aconcagua seems to be barriers, that they could be only delimitating the current distribution of the lineages but not promoted divergence by vicariance as suggest the topology and phylogenetic relationships of our results because T. e. coquimbensis and Aconcagua lineage from opposite banks of Quilimarí and Aconcagua lineage and T. e. elegans from opposite banks of Aconcagua river are not sister clades (Fig. 2, Fig. S1 and Fig. S2). Probably, the current population of each clade is enclosed in particular patches avoiding the aridity. Therefore, the scenario of permeable barriers is also possible, but have not been detected due to the elapsed time or because these lineages have not crossed the rivers since they are in its habitat distribution avoiding the aridity. In the future its necessary to evaluate explicitly the synergistic effect of topography, glaciations and rivers in the phylogeographic structure of more Chilean species from Mediterranean zone of Chile. The Andean and Coastal range, multiple ice sheet glacial advances and retreats and increases in level water volumes due to melting ice probably influenced terrestrial communities in this region. As such, widely distributed endemic species as T. elegans is a good model to assess the joint effects of topography, glacial cycles, and changes in the river water volumes on its genetic differentiation and phylogeographic structure of T. elegans lineages [36, 52, 97].

Taxonomic implications

Apparently, the intraspecific diversity of T. elegans has been historically underrated, and our evidence shows six clearly differentiated genetic lineages. The Loa lineage was previously reported [19, 20], meanwhile a drastic reduction of distributional range was reported in T. e. elegans and an increase to coastal areas from Atacama and Coquimbo region in T. e. coquimbensis [20]. However, the Aconcagua, South 1 and South 2 are newly lineages reported in this study (Figs. 2 and 3, Fig. S1 and Fig. S2).

In general, the genetic distance for species of the genus Thylamys are between 2.5 and 20 % [18, 19, 98]. In our case, the values observed in the genetic differences for the six lineages of T. elegans was between 2 and 11.9 % For example, we are reporting a genetic distance of 9.7 % between the northern and southern clades (Table 1) which is even higher than 5.4 % between T. elegans “north” and T. elegans “south” detected by [19] or higher than linages found within of T. pallidior (5 %), T. venustus (5.4-3.9 %), and T. sponsorious (2.5 %) [18]. However, a study with 82 marsupial species reported that 95 % of cyt b interspecies genetic distances in marsupials have values between 9 % and 16 % with a mean of 12.3 % [99].

Therefore, our results are suggesting a cryptic taxonomic scenario which should be approached by integrative evidence considering species delimitation species analyses, other genes and/or morphological characters. The evidence presented is only the starting point to highlight the deep genetic structure within T. elegans and for the moment, our study is a simple call for futures accurate taxonomic studies on this endemic mouse opossum.

Conclusions

Biogeographic history of T. elegans was shaped mainly for changes of the rivers water levels during the Pliocene and Pleistocene glaciations modulating the genetic differentiation of its lineages. Our results sustain a comprehensive overview suggesting how and when the genetic diversity in T. elegans was structured in the past. We found different intensity of the phylogeographic determinants in the northern and southern clades. For the first time we reported the effects of the Maipo, Mataquito and Teno rivers on the genetic structure and lineage divergence of an endemic small mammal of Chile as primary riverine divergence. While the Quilimarí and Aconcagua rivers were barriers to dispersal, acting as actual geographic boundary and geographic barriers preventing secondary contact in periods of demography and geographic expansion such a secondary riverine divergence. Therefore, rivers must be considered as dynamic barriers that fluctuate over time, have been effective barriers to gene flow. However, the Maipo river is a strong barrier which produced the deep divergence between the northern and southern clades.

Other important barriers could be the final uplift of the Andes, the mountain ranges and the transverse valleys formation. We also found a synergistic role of the climatic changes, hyperaridity, glaciations and mountain ranges formations as biogeographic factors, in the origin and preservation of the genetic divergence of T. elegans suggesting effects of several events and a complex regional history in Chilean Mediterranean zone. All these factors structured deeply the genetic diversity into T. elegans which is composed by six lineages distributed latitudinally and whose genetic distance is suggesting a cryptic complex. This study is only an open window for deeper and detailed studies into this endemic mouse opossum.

Availability of data and materials

Please contact author for data request.

Abbreviations

ML:

Maximum Likelihood

BI:

Bayesian Inference

HPD:

Highest Posterior Density

MCMC:

Markov Chain Monte Carlo

BIC:

Bayesian Information Criterion

HKY:

Hasegawa Kishino Yano

MYA:

Million Years Ago

GTR:

General Time Reversible

GPG:

Great Patagonian Glaciation

CPG:

Coldest Pleistocene Glaciation

SAG:

Servicio Agrícola y Ganadero

CONAF:

Corporación Nacional Forestal

References

  1. Wallace AR. On the monkeys of the Amazon. Proc Zool Soc London. 1852;20:107–10.

    Google Scholar 

  2. Patton JL, da Silva MF. Rivers, refuges, and ridges: the geography of speciation of Amazonian mammals. In: Howard D, Berlocher S, editors. Endless forms: modes and mechanisms of speciation. Oxford: Oxford University Press; 1998. p. 202–13.

    Google Scholar 

  3. Bonvicino CR, Weksler M. Speciation in Amazonia: patterns and predictions of a network of hypotheses. In: Patterson BD, Costa EP, editors. Bones, clones and biomes. Chicago: University of Chicago Press; 2012. p. 283–306.

    Google Scholar 

  4. Patton JL, Da Silva MNF, Malcolm JR. Mammals of the Rio Jurua and the evolutionary and ecological diversification of Amazonia. Bull Am Museum Nat Hist. 2000;244:1–306.

    Article  Google Scholar 

  5. Maldonado-Coelho M, Blake JG, Silveira LF, Batalha-Filho H, Ricklefs RE. Rivers, refuges and population divergence of fire-eye antbirds (Pyriglena) in the Amazon Basin. J Evol Biol. 2013;26:1090–107.

    Article  CAS  PubMed  Google Scholar 

  6. Jansa SA, Barker FK, Voss RS. The early diversification history of didelphid marsupials: A window into south America’s “splendid isolation.” Evolution. 2014;68:684–95.

    Article  PubMed  Google Scholar 

  7. Gardner AL. Mammals of South America, vol. 1. Marsupials, xenarthrans, shrews, and bats. Chicago: Chicago University Press; 2008.

    Book  Google Scholar 

  8. Patton JL, da Silva MNF. Definition of species of pouched four-eyed opossums (Didelphidae, Philander). J Mammal. 1997;78:90–102.

    Article  Google Scholar 

  9. Faria MB, de Oliveira JA, Bonvicino CR. Filogeografia de populações brasileiras de Marmosa (Marmosa) murina (Didelphimorphia, Didelphidae). Rev Nord Biol. 2014;21:27–52.

    Google Scholar 

  10. Guimarães RR, Rocha RG, Loss AC, Mendes-Oliveira AC, Patterson BD, Costa LP. Morphological and molecular discordance in the taxonomic rearrangement of the Marmosops pinheiroi complex (Marsupialia: Didelphidae). Syst Biodivers. 2021;0(0):1–12. Published online: 04 Jun 2021.

  11. Chemisquy MA, Flores DA. Taxonomy of the southernmost populations of Philander (Didelphimorphia, Didelphidae), with implications for the systematics of the genus. Zootaxa. 2012;3481:60–72.

    Article  Google Scholar 

  12. De la Sancha NU, D’Elía G, Teta P. Systematics of the subgenus of mouse opossums Marmosa (Micoureus) (Didelphimorphia, Didelphidae) with noteworthy records from Paraguay. Mamm Biol. 2012;77:229–36.

    Article  Google Scholar 

  13. Faria MB, Nascimento FF, de Oliveira JA, Bonvicino CR. Biogeographic determinants of genetic diversification in the mouse opossum Gracilinanus agilis (Didelphimorphia: Didelphidae). J Hered. 2013;104:613–26.

    Article  CAS  PubMed  Google Scholar 

  14. Fegies AC, Carmignotto AP, Perez MF, Guilardi MD, Lessinger AC. Molecular Phylogeny of Cryptonanus (Didelphidae: Thylamyini): evidence for a recent and complex diversification in South American open biomes. Mol Phylogenet Evol. 2021;162:107213.

    Article  PubMed  Google Scholar 

  15. de la Sancha NU, D’Elía G. Additions to the Paraguayan mammal fauna: the first records of two marsupials (Didelphimorphia, Didelphidae) with comments on the alpha taxonomy of Cryptonanus and Philander. Mammalia. 2015;79:343–56.

    Google Scholar 

  16. Sartorato Zanchetta L, Gomes Rocha R, Reis Leite YL. Comparative phylogeography and demographic history of two marsupials of the Atlantic Forest in eastern Brazil. J Zool Syst Evol Res. 2019;57:632–41.

    Article  Google Scholar 

  17. Teta P, D’Elía G, Flores D, de La Sancha N. Diversity and distribution of the mouse opossums of the genus Thylamys (Didelphimorphia, Didelphidae) in north-eastern and central Argentina. Gayana. 2009;73:180–99.

    Google Scholar 

  18. Giarla TC, Voss RS, Jansa SA. Hidden diversity in the Andes: comparison of species delimitation methods in montane marsupials. Mol Phylogenet Evol. 2014;70:137–51.

    Article  PubMed  Google Scholar 

  19. Palma RE, Boric-Bargetto D, Jayat JP, Flores DA, Zeballos H, Pacheco V, Cancino RA, Alfaro FD, Rodríguez-Serrano E, Pardiñas UFJ. Molecular phylogenetics of mouse opossums: new findings on the phylogeny of Thylamys (Didelphimorphia, Didelphidae). Zool Scr. 2014;43:217–34.

  20. Boric-Bargetto D, Zúñiga-Reinoso Á, Cancino RA, González-Acuña D, Rodríguez-Serrano E, Palma RE, Hernández CE. Phylogenetic evaluation of taxonomic definition of didelphid mouse opossum of the genus Thylamys from valleys of Coquimbo region, Chile. Zootaxa. 2016;4105:339–52.

    Article  PubMed  Google Scholar 

  21. Osgood WH. The mammals of Chile. Chicago: Field Museum of Natural History, Zoology Series; 1943.

  22. Greer JK. Mammals of Malleco province, Chile. Publ Museum, Michigan State Univ Biol Ser. 1965;3:49–152.

    Google Scholar 

  23. Mann G. Los pequeños mamíferos de Chile. Gayana Zool. 1978;40:1–342.

    Google Scholar 

  24. Palma RE. Thylamys elegans. Mamm Species. 1997;582:1–4.

    Article  Google Scholar 

  25. Palma RE, Rivera-Milla E, Yates TL, Marquet PA, Meynard AP. Phylogenetic and biogeographic relationships of the mouse opossum Thylamys (Didelphimorphia, Didelphidae) in southern South America. Mol Phylogenet Evol. 2002;25:245–53.

    Article  Google Scholar 

  26. Luebert F, Pliscoff P. Sinopsis bioclimática y vegetacional de Chile. Santiago de Chile: Editorial Universitaria; 2006.

    Google Scholar 

  27. Armesto JJ, Aroyo MTK, Hinojosa F. The Mediterranean Environment of Central Chile. In: Veblen TT, Young KR, Orme AR, editors. The physical geography of South America. New York: Oxford University Press; 2007. p. 184–99.

  28. Meserve PL, Gómez-González S, Kelt DA. The Chilean Matorral: Characteristics, Biogeography, and Disturbance. In: Goldstein MI, DellaSala DA, editors. Encyclopedia of the world’s biomes. Amsterdam, the Netherlands: Elsevier Academic Press; 2020. p. 594–601.

    Chapter  Google Scholar 

  29. Pine RH, Miller SD, Schamberger ML. Contributions to the mammalogy of Chile. Mammalia. 1979;43:339–76.

    Article  Google Scholar 

  30. Meserve PL, Glanz WE. Geographical Ecology of Small Mammals in the Northern Chilean Arid Zone. J Biogeogr. 1978;5:135.

    Article  Google Scholar 

  31. Tate GHH. Brief diagnoses of twenty-six apparently new forms of Marmosa (Marsupialia) from South America. Am Museum Novit. 1931;493:1–14.

    Google Scholar 

  32. Tate GHH. Systematic revision of the marsupial genus Marmosa, with a discussion of the adaptative radiation of the murine-opossums. Bull Am Museum Nat Hist. 1933;66:1–250.

    Google Scholar 

  33. Giarla TC, Voss RS. DNA Sequence Data from the Holotype of Marmosa elegans coquimbensis Tate, 1931 (Mammalia: Didelphidae) Resolve its Disputed Relationships. Am Museum Novit. 2020;3946:1–8.

  34. Meynard AP, Palma RE, Rivera-Milla E. Phylogeographic relationships of the Chilean llacas of the genus Thylamys (Marsupialia, Didelphidae) based on sequences of the cytochrome b mitochondrial gene. Rev Chil Hist Nat. 2002;75:299–306.

    Google Scholar 

  35. Sallaberry-Pincheira N, Garin CF, González-Acuña D, Sallaberry MA, Vianna JA. Genetic divergence of Chilean long-tailed snake (Philodryas chamissonis) across latitudes: Conservation threats for different lineages. Divers Distrib. 2011;17:152–62.

    Article  Google Scholar 

  36. Muñoz-Mendoza C, D’Elía G, Panzera A, Méndez T. MA, Villalobos-Leiva A, Sites JW, Victoriano PF. Geography and past climate changes have shaped the evolution of a widespread lizard from the Chilean hotspot. Mol Phylogenet Evol. 2017;116:157–71.

    Article  PubMed  Google Scholar 

  37. Torres-Pérez F, Lamborot M, Boric-Bargetto D, Hernández CE, Ortiz JC, Palma RE. Phylogeography of a mountain lizard species: an ancient fragmentation process mediated by riverine barriers in the Liolaemus monticola complex (Sauria:Liolaemidae). J Zool Syst Evol Res. 2007;45:72–81.

    Article  Google Scholar 

  38. Vásquez D, Correa C, Pastenes L, Palma R, Méndez MA. Low phylogeographic structure of Rhinella arunco (Anura:Bufonidae), an endemic amphibian from the Chilean Mediterranean hotspot. Zool Stud. 2013;52:35.

    Article  Google Scholar 

  39. Viruel J, Catalán P, Segarra-Moragues JG. Latitudinal environmental niches and riverine barriers shaped the phylogeography of the central chilean cndemic Dioscorea humilis (Dioscoreaceae). PLoS One. 2014;9:e110029.

    Article  PubMed  PubMed Central  Google Scholar 

  40. Lamborot M, Eaton LC. The Maipo River as a biogeographical barrier to Liolaemus monticola (Tropiduridae) in the mountain ranges of central Chile. J Zool Syst Evol Res. 1997;35:105–11.

    Article  Google Scholar 

  41. Araya-Donoso R, Torres-Pérez F, Véliz D, Lamborot M. Hybridization and polyploidy in the weeping lizard Liolaemus chiliensis (Squamata: Liolaemidae). Biol J Linn Soc. 2019;128:963–74.

    Google Scholar 

  42. Alfaro FM, Muñoz-Ramírez CP, Zúñiga-Reinoso A, Trewick SA, Méndez MA. Phylogeography of the Chilean red cricket Cratomelus armatus (Orthoptera: Anostostomatidae) reveals high cryptic diversity in central Chile. Biol J Linn Soc. 2018;123:712–27.

    Article  Google Scholar 

  43. Lavandero B, Miranda M, Ramírez CC, Fuentes-Contreras E. Landscape composition modulates population genetic structure of Eriosoma lanigerum (Hausmann) on Malus domestica Borkh in central Chile. Bull Entomol Res. 2009;99:97–105.

    Article  CAS  PubMed  Google Scholar 

  44. Chesser RT. Molecular Systematics of the Rhinocryptid Genus Pteroptochos. Condor. 1999;101:439–46.

    Article  Google Scholar 

  45. Vásquez M, Torres-Pérez F, Lamborot M. Genetic variation within and between four chromosomal races of Liolaemus monticola in Chile. Herpetol J. 2007;17:149–60.

    Google Scholar 

  46. Cadenillas R, D’Elía G. Taxonomic revision of the populations assigned to Octodon degus (Hystricomorpha: Octodontidae): With the designation of a neotype for Sciurus degus G. I. Molina, 1782 and the description of a new subspecies. Zool Anz. 2021;292:14–28.

    Article  Google Scholar 

  47. Valdez L, Quiroga-Carmona M, D’Elía G. Genetic variation of the Chilean endemic long-haired mouse Abrothrix longipilis in a geographical and environmental context. PeerJ. 2020;8:e9517.

    Article  PubMed  PubMed Central  Google Scholar 

  48. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J. Biodiversity hotspots for conservation priorities. Nature. 2000;403:853–8.

    Article  CAS  PubMed  Google Scholar 

  49. Sauquet H, Weston PH, Anderson CL, Barker NP, Cantrill DJ, Mast AR, Savolainen V. Contrasted patterns of hyperdiversification in Mediterranean hotspots. Proc Natl Acad Sci U S A. 2009;106:221–5.

    Article  CAS  PubMed  Google Scholar 

  50. Lamborot M, Ossa CG, Vásquez M. Population cytogenetics of the “Northern Mod 1” chromosomal race of Liolaemus monticola Müller & Helmich (Iguanidae) from Central Chile. Gayana. 2012;76:10–21.

    Google Scholar 

  51. Larrea-Meza S, Pinto P, Collado GA, Zúñiga-Reinoso A. A new species of Psectrascelis (Coleoptera: Tenebrionidae: Pimeliinae) from the coastal dunes of the Atacama Desert, Chile. Zootaxa. 2020;4845:109–18.

    Article  Google Scholar 

  52. Victoriano PF, D’Elía G. Evolving in islands of mud: old and structured hidden diversity in an endemic freshwater crayfish from the Chilean hotspot. Sci Rep. 2021;11:1–16.

    Article  Google Scholar 

  53. Valdez L, D’Elía G. Genetic Diversity and Demographic History of the Shaggy Soft-Haired Mouse Abrothrix hirta (Cricetidae; Abrotrichini). Front Genet. 2021;12:184.

    Article  Google Scholar 

  54. Ossa PG, Pérez F, Armesto JJ. Phylogeography of two closely related species of Nolana from the coastal Atacama Desert of Chile: post-glacial population expansions in response to climate fluctuations. J Biogeogr. 2013;40:2191–203.

    Article  Google Scholar 

  55. Ceccarelli FS, Pizarro-Araya J, Ojanguren-Affilastro AA. Phylogeography and population structure of two Brachistosternus species (Scorpiones: Bothriuridae) from the Chilean coastal desert - the perils of coastal living. Biol J Linn Soc. 2017;120:75–89.

    Google Scholar 

  56. Sikes RS, Animal Care and Use Committee of the American Society of Mammalogists. Guidelines of the American Society of Mammalogists for the use of wild mammals in research and education. J Mammal. 2016;97:663–88.

    Article  PubMed  PubMed Central  Google Scholar 

  57. Longmire JL, Lewis AK, Brown NC, Buckingham JM, Clark LM, Jones MD, Meincke LJ, Meyne J, Ratliff RL, Ray FA, Wagner RP, Moyzis RK. Isolation and molecular characterization of a highly polymorphic centromeric tandem repeat in the family Falconidae. Genomics. 1988;2:14–24.

    Article  CAS  PubMed  Google Scholar 

  58. Giarla TC, Voss RS, Jansa SA. Species limits and phylogenetic relationships in the didelphid marsupial genus Thylamys based on mitochondrial DNA sequences and morphology. Bull Am Museum Nat Hist. 2010;346:1–67.

    Article  Google Scholar 

  59. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999;41:95–8.

    CAS  Google Scholar 

  60. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;25:4876–82.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25:1451–2.

    Article  CAS  PubMed  Google Scholar 

  62. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Mol Biol Evol. 2015;32:268–74.

    Article  CAS  PubMed  Google Scholar 

  63. Trifinopoulos J, Nguyen L-T, von Haeseler A, Minh BQ. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 2016;44:W232–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol Biol Evol. 2017;35:518–22.

    Article  PubMed Central  Google Scholar 

  66. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. Mrbayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61:539–42.

    Article  PubMed  PubMed Central  Google Scholar 

  67. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 2016;33:1870–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Guillot G, Mortier F, Estoup A. Geneland: a computer package for landscape genetics. Mol Ecol Notes. 2005;5:712–5.

    Article  CAS  Google Scholar 

  69. Gelman A, Carlin JB, Stern HS, Rubin DB. Bayesian Data Analysis. 2nd edition. London: Chapman and Hall; 1995.

  70. Guillot G, Santos F, Estoup A. Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interface. Bioinformatics. 2008;24:1406–7.

    Article  CAS  PubMed  Google Scholar 

  71. Bouckaert R, Heled J, Kuhnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2014;10:e1003537.

    Article  PubMed  PubMed Central  Google Scholar 

  72. Rambaut A, Suchard MA, Xie D, Drummond AJ. Tracer v1.6. 2014. http://beast.bio.ed.ac.uk/Tracer. Accessed 7 Jan 2020.

  73. Rambaut A, Drummond AJ. TreeAnnotator v1.7.0. 2013. beast.-bio.ed.ac.uk/TreeAnnotator. Accessed 7 Jan 2020.

  74. Rambaut A. FigTree: tree figure drawing tool, v1.4.2. 2012. http://tree.bio.ed.ac.uk/software/figtree/. Accessed 7 Jan 2020.

  75. Sarricolea P, Meseguer Ruiz O, Romero-Aravena H. Precipitation trends in the Chilean Norte Grande and its relationships with climate change projections. Diálogo Andin. 2017;54:41–50.

    Article  Google Scholar 

  76. Juliá C, Montecinos S, Maldonado A. Características Climáticas de la Región de Atacama. In: Squeo FA, Arancio, G. & Gutiérrez JR, editors. Libro Rojo de la Flora Nativa y de Los Sitios Prioritarios para su Conservación: Región de Atacama. La Serena, Chile: Ediciones Universidad de La Serena; 2008. p. 25–42.

    Google Scholar 

  77. Haselton K, Hilley G, Strecker MR. Average Pleistocene climatic patterns in the southern central Andes: Controls on mountain glaciation and paleoclimate implications. J Geol. 2002;110:211–26.

    Article  Google Scholar 

  78. Roberts NJ, Barendregt RW, Clague JJ. Pliocene and Pleistocene chronostratigraphy of continental sediments underlying the Altiplano at La Paz, Bolivia. Quat Sci Rev. 2018;189:105–26.

    Article  Google Scholar 

  79. Charrier R, Pinto L, Rodríguez M. Tectonostratigraphic evolution of the andean orogen in Chile. In: T. Moreno WG, editor. The Geology of Chile. London: The Geological Society; 2007. p. 21–116.

  80. Farías M, Charrier R, Carretier S, Martinod J, Fock A, Campbell D, Cáceres J, Comte D. Late Miocene high and rapid surface uplift and its erosional response in the Andes of central Chile (33°-35°S). Tectonics. 2008;27:TC1005.

    Article  Google Scholar 

  81. Hinojosa LF, Villagrán C. History of the southern South American forests.1. paleobotanical, geological and climatical background on Tertiary of southern South America. Rev Chil Hist Nat. 1997;70:225–39.

    Google Scholar 

  82. Zachos J, Pagani H, Sloan L, Thomas E, Billups K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science. 2001;292:686–93.

    Article  CAS  PubMed  Google Scholar 

  83. Elderfield H, Ferretti P, Greaves M, Crowhurst S, McCave IN, Hodell D, Piotrowski AM. Evolution of Ocean Temperature and Ice Volume Through the Mid-Pleistocene Climate Transition. Science. 2012;337:704–9.

    Article  CAS  PubMed  Google Scholar 

  84. Lisiecki LE, Raymo ME. A Pliocene-Pleistocene stack of 57 globally distributed benthic δ 18 O records. Paleoceanography. 2005;20:PA1003.

    Google Scholar 

  85. Clark PU, Archer D, Pollard D, Blum JD, Rial JA, Brovkin V, Mix AC, Pisias NG, Roy M. The middle Pleistocene transition: characteristics, mechanisms, and implications for long-term changes in atmospheric pCO2. Quat Sci Rev. 2006;25:3150–84.

    Article  Google Scholar 

  86. Rabassa J, Coronato AM, Salemme M. Chronology of the Late Cenozoic Patagonian glaciations and their correlation with biostratigraphic units of the Pampean region (Argentina). J South Am Earth Sci. 2005;20:81–103.

    Article  Google Scholar 

  87. Turner KJ, Fogwill CJ, McCulloch RD, Sugden DE. Deglaciation of the eastern flank of the North Patagonian Icefield and associated continental-scale lake diversions. Geogr Ann Ser A Phys Geogr. 2005;87:363–74.

  88. Zemlak TS, Habit EM, Walde SJ, Battini MA, Adams EDM, Ruzzante DE. Across the southern Andes on fin: glacial refugia, drainage reversals and a secondary contact zone revealed by the phylogeographical signal of Galaxias platei in Patagonia. Mol Ecol. 2008;17:5049–61.

    Article  CAS  PubMed  Google Scholar 

  89. Clapperton CM. Quaternary glaciations in the southern hemisphere: An overview. Quat Sci Rev. 1990;9:299–304.

    Article  Google Scholar 

  90. Rabassa J, Clapperton CM. Quaternary glaciations of the southern Andes. Quat Sci Rev. 1990;9:153–74.

    Article  Google Scholar 

  91. Clapperton CM. The quaternary glaciation of Chile: a review. Rev Chil Hist Nat. 1994;67:369–83.

    Google Scholar 

  92. Jordan TE, Kirk-Lawlor NE, Blanco NP, Rech JA, Cosentino NJ. Landscape modification in response to repeated onset of hyperarid paleoclimate states since 14 Ma, Atacama Desert, Chile. Bull Geol Soc Am. 2014;126:1016–46.

    Article  CAS  Google Scholar 

  93. McCulloch RD, Bentley MJ, Purves RS, Hulton NRJ, Sugden DE, Clapperton CM. Climatic inferences from glacial and palaeoecological evidence at the last glacial termination, southern South America. J Quat Sci. 2000;15:409–17.

    Article  Google Scholar 

  94. Zúñiga-Reinoso A, Predel R. Past climatic changes and their effects on the phylogenetic pattern of the Gondwanan relict Maindronia (Insecta: Zygentoma) in the Chilean Atacama Desert. Glob Planet Change. 2019;182:103007.

    Article  Google Scholar 

  95. Zúñiga-Reinoso A, Pinto P, Predel R. A New Species of Gyriosomus Guérinmeneville (Coleoptera: Tenebrionidae) from the Chilean Atacama Desert. Ann Zool. 2019;69:105–12.

    Article  Google Scholar 

  96. Brüggen J. Fundamentos de la geología de Chile. Santiago, Chile: Instituto Geográfico Militar; 1950.

    Google Scholar 

  97. Victoriano PF. Phylogeography of Chilean Lizards: Histories of Genetic Diversification on the Western Slope of Southern Andes. In: Morando M, Ávila LJ, editors. Lizards of Patagonia. Natural and Social Sciences of Patagonia. Springer, Cham; 2020. p. 255–91.

    Google Scholar 

  98. Patton JL, Dos Reis SF, Da Silva MNF. Relationships among didelphid marsupials based on sequence variation in the mitochondrial cytochrome B gene. J Mamm Evol. 1996;3:3–29.

    Article  Google Scholar 

  99. Schrago CG, Mello B. Employing statistical learning to derive species-level genetic diversity for mammalian species. Mamm Rev. 2020;50:240–51.

    Article  Google Scholar 

Download references

Acknowledgements

We thank to Jaime Zúñiga, Claudio Correa and Dayana Vásquez for fieldwork and to Carlos Guerra, Cristián Larraguibel and project “Diagnóstico de Sitios de Alto Valor para la Conservación en la Región de Valparaíso, Fase II. Línea 3: Sitios Punta Curaumilla – Las Docas y Los Molles – Pichidangui.” Código BIP N°30137941-0, Francisco Santander and Alfonso Jara for the yacas pictures from the Loa river Mouth (Fig. 1a), Los Molles (Fig. 1c), Punta Curaumilla (Fig. 1d), Lipimávida (Fig. 1e) and the Nahuelbuta Coastal range, Bío-Bío region (Fig. 1f). We thank to Servicio Agrícola y Ganadero (SAG) and Corporación Nacional Forestal (CONAF) for trapping permits and the Bioethics Committee of Pontificia Universidad Católica de Chile and Universidad de Concepción for your approval. We thank to Laboratorio de Ecología Evolutiva y Filoinformática, Universidad de Concepción; Laboratorio de Biología Evolutiva, Pontificia Universidad Católica de Chile; Laboratorio de Zoología, Epidemiología y Evolución, Pontificia Universidad Católica de Valparaíso and to Chilean Hantavirus Crew for collecting several of specimens analyzed in this study. DBB appreciates funding of his postdoctoral project ANID/CONICYT + FONDECYT 3180237 and support of its sponsor Fernando Torres Pérez ANID/ CONICYT + FONDECYT 1171280. We acknowledge the loan of Colección Profesor Patricio Sánchez Reyes, his curator Patricio Zavala and from Guillermo D’Elía (GD1131, GD1132 samples) and Ulyses Pardiñas (UP397 sample) mentioned in Appendix I. We dedicate this study to our co-author Daniel González-Acuña which died before to see this manuscript published.

Funding

Financial support was provided by Graduate School of Universidad de Concepción, Doctorado en Sistemática y Biodiversidad, CONICYT Doctoral Fellowship (2011), postdoctoral project 2015-2017 VRIEA PUCV and ANID/CONICYT + FONDECYT 3180237 (DBB), ANID/CONICYT + FONDECYT 1170815, 1201506 (CEH), ANID/CONICYT + FONDECYT 1170486 (ERS), ANID/CONICYT + FONDECYT 1170972 (DGA) and ANID/CONICYT + FONDECYT 1170761 (REP).

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Author notes

  1. Daniel González-Acuña is deceased.

Authors and Affiliations

  1. Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, 2373223, Casilla, Valparaíso, Chile

    Dusan Boric-Bargetto

  2. Zoological Institute, Faculty of Mathematics and Natural Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany

    Álvaro Zúñiga-Reinoso

  3. Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Barrio Universitario s/n. Concepción, Santiago, Chile

    Oscar Inostroza-Michel, Enrique Rodríguez-Serrano & Cristián E. Hernández

  4. Laboratorio de Parásitos y Enfermedades de Fauna Silvestre, Facultad de Ciencias Veterinarias, Universidad de Concepción, Concepción, Chile

    Daniel González-Acuña

  5. Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8380453, Santiago, Chile

    R. Eduardo Palma

  6. Universidad Católica de Santa María, Arequipa, Peru

    Cristián E. Hernández

Authors
  1. Dusan Boric-Bargetto
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  2. Álvaro Zúñiga-Reinoso
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  3. Oscar Inostroza-Michel
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Contributions

Conceived and designed the experiments: DBB, REP, CEH, AZR. Performed the experiments: DBB. Analyzed the data: DBB, AZR, ERS, OIM. Contributed reagents/materials/analysis tools: REP, CEH, DGA. Wrote the paper: DBB, REP, AZR. Critically evaluated the manuscript: DBB, AZR, ERS, CEH, REP, DGA, OIM. The author(s) read and approved the final manuscript.

Corresponding author

Correspondence to Dusan Boric-Bargetto.

Ethics declarations

Ethics approval

Captures were made under the following permits granted by Servicio Agrícola y Ganadero (SAG): 1607-2012, 6134-2011, 1158/2011, 17/2000, 7325/2005, 1056/1999) and Corporación Nacional Forestal (CONAF): 10-02/2002, 13-03/2003, 14-99/2004, 24/2004, 07-06/2006) and the approval of the Bioethics Committee of Pontificia Universidad Católica de Chile and Universidad de Concepción.

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Not applicable.

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The authors declare that they have no competing interests.

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Supplementary Information

Additional file 1: Appendix I.

Haplotypes, catalog number of each voucher, Sample type, GenBank access number, collection localities, coordinates and reference. Reference 1 [19], 2 (this study), 3 [20] and 4 [58]. * = GenBank sequences from references 1, 3 and 4. SSUC: Colección flora y fauna, Profesor Patricio Sánchez Reyes. NK: voucher from MSB Museum of Southwestern Biology and SSUC, UCK: Kryovoucher Catholic University, CZZA-UTA: Colección zoológica de zonas áridas y andinas, CNP: Centro Nacional Patagónico, GD: Guillermo D'Elía, EP: Eduardo Palma. UP: Ulyses Pardiñas. III14, III70 and IV62: Daniel González-Acuña. NK96072 correspond to T. pallidior A and UP397 to T. pallidior B.

Additional file 2: Fig. S1.

The maximum likelihood haplotype tree with the six lineages of T. elegans. The phylogeny by ML for the six lineages in T. elegans based on 49 cyt-b haplotypes. Numbers of nodes are bootstrap values for ML and posterior probability for BI. Loa (Clade A); T. e. coquimbensis (Clade B); Aconcagua (Clade C); T. e. elegans (Clade D); South 1 (Clade E); South 2 (Clade F). Terminal labels are as follow: haplotype number, locality number, number of specimens sharing haplotypes. Locality numbers correspond to Fig. 2 and Appendix I. Haplotype numbers are given in Appendix I. The ML and BI phylogenies were rooted using T. pallidior A and T. pallidior B as outgroup.

Additional file 3: Fig. S2.

The maximum likelihood tree with the six lineages of T. elegans. The phylogeny by ML for the six lineages of T. elegans based on 95 cyt-b sequences. Numbers of nodes are bootstrap values for ML and posterior probability for BI. Loa (Clade A); T. e. coquimbensis (Clade B); Aconcagua (Clade C); T. e. elegans (Clade D); South 1 (Clade E); South 2 (Clade F). Terminal labels show localities are as follow. The ML and BI phylogenies were rooted using T. pallidior A and T. pallidior B as outgroup. Northern clade encompasses the Loa, T. e. coquimbensis, Aconcagua and T. e. elegans lineages while the southern clade encompasses the South 1 and South 2 lineages.

Additional file 4: Fig. S3.

Divergence times of the six lineages in T. elegans. Clades correspond to Fig. 2. Number of nodes are average values and bars in purple are the 95% HPD. A time scale show the geological ages. Bluish shaded areas represent the GPG (~1.68-1.016 Mya) and the CPG (~0.7-0.6 Mya). Arrows show two points of calibrations previously reported as time divergence estimates of T. elegans-T. pallidior and T. tatei-T. sp [19]. Thylamys tatei (MUSM23253, KF164556) and Thylamys sp (MUSA1787, KF164542) were used as outgroups [19].

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Boric-Bargetto, D., Zúñiga-Reinoso, Á., Inostroza-Michel, O. et al. A comprehensive overview of the genetic diversity in Thylamys elegans (Didelphimorphia: Didelphidae): establishing the phylogeographic determinants. Rev. Chil. de Hist. Nat. 94, 5 (2021). https://doi.org/10.1186/s40693-021-00103-5

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Revista Chilena de Historia Natural

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